September 30, 2024

Rare Genetic Disorder

UNC Fast-Tracks Personalized Treatment for Twins with Ultra Rare Genetic Disorder


In May 2022, Yael Shiloh-Malawsky, MD, a neurologist at the UNC School of Medicine, met two new patients combatting a rare and fatal neurodegenerative disorder called Batten disease. With help from UNC, the twin girls were able to get personalized treatment from bench to bedside in record time.

When Karen and David Kahn’s daughters, Amelia and Makenzie, were born in 2010, they knew life with twins would be different. But after just 18 months, the Kahn family was forced onto an unexpected and harrowing path.

Amelia began failing her speech and behavior milestones. At age two, she was diagnosed with autism. Then, at 7-years-old, both girls started experiencing unexplained vision loss and were declared legally blind.

Desperate to find a diagnosis, the Kahns reached out to a geneticist for testing, eventually learning that both girls had an extremely rare and progressive genetic disorder of the nervous system called juvenile Batten disease, or CLN3, for which there is no cure.

They refused to give in to the disease and worked to find a treatment, and now – seven years after diagnosis – the family is part of a first-in-kind clinical study at UNC Health, led by Yael Shiloh-Malawsky, MD, associate professor of neurology.
A New, Personalized Treatment for Two

Juvenile Batten disease is a rare neurodegenerative condition affecting as little as 1 of every 100,000 births. Around the age of six or seven, patients typically begin experiencing vision loss, followed by paralysis, cognitive decline, seizures, and loss of speech. Because the condition causes rapid brain cell death, life expectancy is from the teens to early twenties.

The disease is linked to genetic changes in a gene called CLN3. Located on chromosome 16, the CLN3 protein, which is encoded by the gene, is important for directing the body to store and break down cellular waste in cellular organs called lysosomes. When this waste builds up in the body’s cells, it causes cell death in the brain and eyes.

The Kahn girls underwent further genetic testing. Geneticists confirmed that Amelia and Makenzie had the common genetic changes seen in CLN3 Batten disease.

But geneticists also found something else. The girls had another genetic variant in the CLN3 gene – one that had never before been observed in a person with Batten disease.

Not long after diagnosis, the Kahns formed the ForeBatten Foundation, a nonprofit that funds juvenile Batten disease research and support for families whose lives have been affected by the disease. It was at this point that the Kahn family reached out to Michelle L. Hastings, PhD, the Pfizer Upjohn Research Professor of Pharmacology at the University of Michigan Medical School, to discuss antisense oligonucleotide treatments.

Hastings has been studying short RNA molecules called antisense oligonucleotides (ASOs) for more than 20 years. Much like a pair of teeny molecular tweezers, the short RNA molecules can target specific sites on genes and correct the gene expression to restore protein function.

By January 2021, Hastings was working on a therapy for pediatric patients with the common CLN3 genetic variant in parallel with a therapy for the Kahn girls’ specific variant. She was able to do this work thanks to newly released guidance from the U.S. Food and Drug Administration (FDA), which gave researchers directions on how to develop individualized investigational ASOs for those with severely debilitating or life-threatening genetic diseases.

This new type of personalized trial, frequently referred to as an “N-of-1” study, is a type of clinical trial that focuses on just one individual rather than a large group of people. In the case of Makenzie and Amelia, the specific treatment is created and tested for two patients, an “N-of-2” study.

Jessica Centa, PhD, a senior postdoctoral research fellow in the Hastings lab, took cells recovered from skin biopsies from both girls, and grew them in culture dishes in the lab and used them to test a series of ASOs to determine which ones were capable of recovering expression from the girls’ mutated gene. They identified a highly potent and effective ASO as their lead candidate for development of personalized treatment.

After researchers developed the ASO drug that had the potential to be effective, it was time to name it. Inspired by the girl’s favorite animals, zebras and monkeys, the customized treatment was named Zebronkysen. With guidance from the ForeBatten Development team, the personalized drug was manufactured and bottled for use.

“Drug development and medicine is changing,” said Hastings, who is also the director of the RNA Therapeutics Initiative at the University of Michigan. “It’s not just drug companies developing drugs for large patient populations. It’s also family members, doctors that are seeing the patients, and basic scientists coming together to apply new technologies to treat disease.

“As we see more success with individualized treatments using ASOs, I think that will drive support, which we hope will lead to more treatments of this kind to children with juvenile Batten disease and other ultra rare conditions.”

A Quick Transition from Bench to Bedside

In May 2022, the Kahn family moved cross-country from Scottsdale, AZ to Chapel Hill, NC to be closer to family. Amelia and Makenzie’s Phoenix neurologist reached out to Dr. Shiloh-Malawsky, an expert in child neurodegenerative disorders at the UNC School of Medicine, to assist in their transition of care to UNC and to establish a new medical home for the girls in North Carolina.

Dr. Shiloh-Malawsky became their new neurologist, forming part of a multidisciplinary team at UNC that helped treat the twins’ myriad symptoms, which included seizures, muscle spasms, and anxiety. However, later in 2022, the disease progressed further. Feeding and mobility became more challenging for the girls, increasing the urgency for treatment.

Fortunately, Hastings’ ASO drug was developed for the specific gene altered in Amelia’s and Makenzie’s genomes. But before Dr. Shiloh-Malawsky could bring the treatment to the clinic, she had to obtain approval from UNC’s Institutional Review Board (IRB), UNC’s Ethics Review Committee, and the FDA. Typically, this process takes a very long time.

“This is not like other study drug approvals, in the sense that the treatment is being created only for these two patients,” said Dr. Shiloh-Malawsky. “Most importantly, we have to do it quickly if we want to help them before they lose any more abilities.”

In spring 2023, the ForeBatten Foundation established the N-of-2 study development team, with UNC serving as the clinical site of the study, and Dr. Shiloh-Malawsky the principal investigator. The team was able to develop the individualized ASO and clinical trial protocol, submit for FDA approval of the new investigational drug, and gain institutional and FDA approvals in a little over a year. The FDA officially approved the new investigational drug in late May 2024.

“This is the first time this kind of N-of-1, or N-of-2, personalized treatment is going through the UNC system,” said Dr. Shiloh-Malawsky. “This is an extraordinary example of how incredible talent, investment, and collaboration with multiple scientists can come together to bring new and innovative treatments to pediatric patients in need. It’s incredible.”

A New Proof of Concept

In June 2024, just two weeks after the study drug was approved by the FDA, Amelia and Makenzie received their first dosages of Zebronkysen. Their ASO drug is provided as an “N-of-2” clinical trial, with UNC serving as the study site.

The drug is injected into the cerebrospinal fluid via spinal tap while the girls are under general anesthesia. The girls’ treatment is provided under a study protocol with close monitoring to assess tolerance to the drug and observe whether it has staved off further neurodegeneration.

Dr. Shiloh-Malawsky is hopeful that restoring the function of Amelia and Makenzie’s CLN3 gene can prevent further decline. If it proves beneficial, the girls will use the drug for the rest of their lives.

But this latest drug development impacts more than just the Kahn family. This study could be used as a proof-of-concept for other personalized treatments to help patients who have other variants in the CLN3 gene, other subtypes of Batten disease, or other pediatric genetic disorders.

“There are other patients who could benefit if a drug affecting the common juvenile Batten mutation was created,” said Dr. Shiloh-Malawsky. “This is why I’m at UNC, to be at a place that has the knowledge, the systems, and the interest in taking scientific advancements and giving applying them to the development of intervention for our patients, giving them hope of treatment.”

It is too early to tell what long-term effects the treatment will have on the girls, but so far, the signs are positive.

“This probably isn’t a cure, and we are aware of that,” said Karen Kahn, mother of Amelia and Makenzie and co-founder of the ForeBatten foundation. “I think this is a major step in the right direction. When there is no treatment available for children, to finally have something with promise, is exciting.”

UNC, personalized treatment, ultra-rare genetic disorder, twins, gene therapy, precision medicine, genomic analysis, genetic sequencing, CRISPR, gene-editing, geneticists, bioinformaticians, clinicians, clinical trials, rare diseases, patient-specific interventions, advocacy, research funding, healthcare solutions, family support.

#UNC, #PersonalizedTreatment, #RareDisease, #GeneTherapy, #PrecisionMedicine, #GenomicAnalysis, #GeneticSequencing, #CRISPR, #GeneEditing, #MedicalInnovation, #ClinicalTrials, #RareGenetics, #HealthcareSolutions, #Bioinformatics, #RareDiseaseResearch, #FamilySupport, #PatientCare, #GeneticsResearch, #AdvocacyForRare, #MedicalBreakthrough

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September 28, 2024

Undiagnosed Genetic Disease

Distant relatedness in biobanks harnessed to identify undiagnosed genetic disease


An innovative analysis of shared segments within the genome — an indication of distant “relatedness” — has identified undiagnosed cases of Long QT syndrome, a rare disorder that can lead to abnormal heart rhythms, fainting and sudden cardiac death.

The findings, reported in the journal Nature Communications, illustrate the feasibility of the new approach developed by researchers at Vanderbilt University Medical Center to detect undiagnosed carriers of rare disease-causing genetic variants.

“Rare genetic diseases are usually studied in referral populations — people who have been referred to specialty clinics for evaluation — but this approach often overestimates the true population impact, which would be better assessed in large non-referral populations, such as biobanks,” said Jennifer (Piper) Below, PhD, professor of Medicine in the Division of Genetic Medicine and senior corresponding author of the new study.

Because most biobanks recruit participants from the same region, there is often significant undocumented relatedness among the participants, resulting in genomic segments that are shared due to common ancestry - “identical-by-descent” segments, Below explained.

“Identical-by-descent segments give us an opportunity to cluster related people to find rare variants that were present in a common ancestor,” she said.

To do this, the researchers developed a genetic inference method called DRIVE (Distant Relatedness for Identification and Variant Evaluation). The studies were led by co-first authors Megan Lancaster, MD, PhD, a clinical fellow in the Division of Cardiovascular Medicine, and Hung-Hsin Chen, PhD, who was a postdoctoral fellow in the Division of Genetic Medicine. Dan Roden, MD, the Sam L. Clark, MD, PhD Chair and Senior Vice President for Personalized Medicine, is co-senior author.

To test DRIVE, the researchers focused on a rare variant in the gene KCNE1 that causes Type 5 Long QT syndrome (LQT5). The KCNE1 gene encodes a protein that modifies potassium currents.

An international consortium of 26 centers had identified 89 probands (affected individuals who are the first subjects of a genetic study) with possible LQT5, 140 additional carrier relatives, and 19 cases of another syndrome attributed to variants in KCNE1.

Of 35 probands with the most common KCNE1 variant (p.Asp76Asn), nine (26%) were evaluated by the Genetic Arrhythmia Clinic at VUMC. None of the probands were known to be related. Three relatives of the probands were also found to carry the variant.

“This enrichment of a rare variant at VUMC relative to other centers in the consortium suggested that these local probands may be distantly related and that we could use that relatedness to identify additional carriers in BioVU,” Below said. BioVU is VUMC’s DNA biobank linked to de-identified electronic health records.

The team first estimated the genome-wide relatedness of the 12 clinically identified p.Asp76Asn carriers and constructed lineage pedigrees. They found eighth to ninth degree relatedness among these pedigrees (for reference, fourth cousins — great-grandchildren of first cousins — are ninth degree relatives), supporting the hypothesis of a local common ancestor with the p.Asp76Asn variant.

Then, the researchers identified shared genomic regions that spanned the KCNE1 gene and applied DRIVE to 69,819 BioVU subjects. They identified 22 BioVU subjects with the shared region, confirmed the p.Asp76Asn variant by DNA sequencing, and assessed electrocardiograms and medical records for features of LQT5.

Both referral and non-referral carriers of the variant have prolonged QT interval compared to controls.

“In this study, we used DRIVE to rapidly pinpoint 22 carriers of a previously described pathogenic gene variant,” Below said. “DRIVE could also be used to identify unknown causal gene variants, by clustering individuals with shared identical-by-descent segments and assessing the enrichment of disease within clusters.

“We’re excited about the potential of DRIVE to identify undiagnosed cases of genetic disease.”

Co-first author Chen is now a tenure-track assistant research fellow of the Institute of Biomedical Science at Academia Sinica in Taiwan and holds a joint faculty appointment at VUMC. Other authors of the Nature Communications study include Benjamin Shoemaker, MD, Matthew Fleming, MD, PhD, Teresa Strickland, James Baker, Grahame Evans, Hannah Polikowsky, David Samuels, PhD, and Chad Huff, PhD.

genetics, DNA, gene, chromosome, heredity, mutation, genotype, phenotype, genetic variation, genome, CRISPR, biotechnology, genetic engineering, molecular biology, epigenetics, SNP, genetic disorder, bioinformatics, population genetics, genomics,

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September 27, 2024

Deadly Genetics of Cholera

Experts discover the deadly genetics of cholera, which could be key to its prevention


Experts have used a cutting-edge computational approach to discover the genetic factors that make the bacteria behind cholera so dangerous—which could be key to preventing this deadly disease.

The breakthrough study, published in Nature Communications, is led by Professor Tania Dottorini from the University of Nottingham, in collaboration with Bangladesh's Institute of Epidemiology, Disease Control and Research (IEDCR), International Center for Diarrheal Disease Research, Bangladesh, and North South University.

The innovative research combines machine learning, genomics, genome-scale metabolic modeling (GSMM), and 3D structural analysis to uncover the genetic secrets of Vibrio cholerae—the bacteria behind cholera.

Cholera is a deadly diarrheal disease that continues to threaten millions worldwide, with up to 4 million cases and as many as 143,000 deaths each year. In Bangladesh alone, where cholera is a persistent danger, 66 million people are at risk, with more than 100,000 cases and 4,500 deaths annually.

Vibrio cholerae, is evolving in ways that make the disease more severe and harder to control, but until now, scientists have struggled to pinpoint the exact genetic factors driving these changes.

There is even less knowledge about the genomic traits responsible for the severity of cholera resulting from these lineages. About 1 in 5 people with cholera will experience a severe condition owing to a combination of symptoms (primarily diarrhea, vomiting, and dehydration).

In this new study, the U.K.-Bangladeshi research team analyzed bacterial samples from cholera patients across six regions in Bangladesh, collected between 2015 and 2021. They identified a set of unique genes and mutations in the most recent and dominant strain of Vibrio cholerae responsible for the devastating 2022 outbreak.

These genetic traits are linked to the bacteria's ability to cause severe symptoms like prolonged diarrhea, intense abdominal pain, vomiting, and dehydration—symptoms that can lead to death in severe cases.

Professor Dottorini said, "By identifying the key genetic factors that drive both the transmission and severity of cholera, we've taken a significant step toward developing more effective treatments and targeted interventions. This could save thousands of lives, not just in Bangladesh, but globally."

The findings of the study also revealed that some of these disease-causing traits overlap with those that help the bacteria spread more easily. The findings show how these genetic factors enable Vibrio cholerae to survive in the human gut, making it more resilient to environmental stress and more efficient at causing disease. This research highlights the complex interactions between the bacteria's genetic makeup and its ability to cause severe illness.

This new computational framework is a major step forward in the fight against cholera. By identifying the key genetic factors that make Vibrio cholerae more dangerous, scientists can develop better treatments and more targeted strategies to control and prevent future outbreaks. This breakthrough offers new hope for improving public health in Bangladesh and potentially saving countless lives worldwide.

Dr. Dottorini adds, "Our findings open the door to a new era of cholera research, where we can develop tools to predict and potentially prevent severe outbreaks before they occur. The ultimate goal is to translate these insights into real-world solutions that protect vulnerable populations.

"This breakthrough was only possible through the close collaboration between our U.K. and Bangladeshi partners. Together, we've combined cutting-edge computational tools with local expertise to tackle one of the most pressing public health challenges."

#CholeraResearch #GeneticBreakthrough #DiseasePrevention #PublicHealth #Vaccines #HealthInnovation #Epidemiology #Microbiology #OutbreakResponse #Therapeutics #GeneticResistance #EnvironmentalHealth #GlobalHealth #HealthStrategies #CholeraOutbreak #VaccineDevelopment #ResearchCommunity #PathogenGenetics #HealthSurveillance #ClinicalResearch

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September 26, 2024

Gene Developmental Disorder

Most new recessive developmental disorder diagnoses lie within known genes, say scientists


Scientists have conducted the largest and most diverse study to date on how recessive genetic changes contribute to developmental disorders. They found that most undiagnosed cases that are due to recessive causes are linked to genes we already know about, and suggest a shift in research focus could improve diagnosis rates.

Researchers from the Wellcome Sanger Institute and their collaborators at GeneDx analyzed genetic data from nearly 30,000 families affected by developmental disorders—six times more families with greater diversity in ancestral backgrounds compared to previous work.

While discovering several genes that were previously not linked to these conditions, researchers found that known genes explain over 80% of cases caused by recessive genetic variants. This is a significant increase from previous estimates. The study also revealed the contribution of recessive genetic variants to developmental disorders varies significantly across the ethnic groups studied.

The findings, published 23 September in Nature Genetics, shed new light on the genetic basis of developmental disorders, and highlight the importance of considering a person's genetic background in diagnosis and research.

The team suggests that efforts to discover recessive genes associated with these disorders in the last few years have been largely successful and that the challenge now lies more in interpreting genetic changes in known recessive genes. Using this approach could potentially be used to diagnose twice as many patients compared to focusing solely on remaining gene discovery, they say.

Many developmental disorders, which can impact a child's physical, intellectual, or behavioral development, have genetic origins. Some are caused by recessive genes, where a child must inherit an altered gene copy from both parents to develop the condition. They include Joubert syndrome, Bardet-Biedl syndrome and Tay-Sachs disease. Until now, overall quantification of these recessive genetic causes across diverse populations has not been done.

In this new study, researchers combined summarized data from the Deciphering Developmental Disorders (DDD) study and GeneDx cohorts to identify individuals with similar genetic backgrounds, totaling 29,745 families. Over 20% of these families were from mostly non-European ancestries. Analyzing this large dataset provided more insight, especially for smaller and less-studied groups.

The team found the number of patients affected by recessive genetic variants varied greatly between different ancestry groups, ranging from two to 19% of cases. This variation is strongly linked to the prevalence of unions between close relatives—consanguinity—in these groups.

Researchers identified several genes, including KBTBD2, CRELD1 and ZDHHC16, newly associated with developmental disorders, providing answers for previously undiagnosed families. They also estimate that around 12.5% of patients may have multiple genetic factors contributing to their condition, highlighting the complexity of these disorders.

Importantly, they found known genes explain about 84% of cases caused by recessive genetic variants, which was similar across individuals from European and non-European ancestry groups.

This substantial increase from previous estimates suggests that the new recessive genes that have been discovered over the last few years account for a substantial fraction of previously undiagnosed patients with recessive causes.

However, the scientists found that there are likely still diagnoses being missed in these known genes that involve DNA changes that are difficult to interpret. The findings emphasize the importance of improving interpretation of harmful genetic variants in known disease-causing genes.

Dr. Kartik Chundru, first author of the study, formerly at the Wellcome Sanger Institute and now University of Exeter, said, "These gene discoveries will provide answers for some previously undiagnosed families and help clinicians better understand and identify these conditions.

"Our study highlights the importance of reanalyzing genetic data with updated methods and knowledge, as it can lead to new diagnoses for patients without needing additional samples."

Dr. Vincent Ustach, senior author of the study at GeneDx, said, "This is the most diverse group of participants ever studied to address the recessive contribution to developmental disorders, and showcases the critical impact that a diverse dataset has for delivering a more comprehensive understanding of developmental disorders across different ancestries.

"Findings from this study can drive more personalized and actionable results for families with affected children, and overall enhances our ability to provide answers for underrepresented populations."

Dr. Hilary Martin, senior author of the study at the Wellcome Sanger Institute, said, "One of the surprising findings from this work was that many patients with one known genetic diagnosis might actually have additional rare genetic changes contributing to their condition.

"Identifying these additional changes could improve our understanding of the patient's condition, lead to more accurate diagnoses, and potentially offer new treatment options. It also highlights the complexity of genetic disorders and the need for comprehensive genetic analysis."

#RecessiveDisorders, #GeneticResearch, #KnownGenes, #Mutations, #Diagnosis, #Treatment, #WholeExomeSequencing, #GeneticCounseling, #CausativeVariants, #TherapeuticStrategies, #GeneticLinks, #EnvironmentalFactors, #DevelopmentalDelays, #HereditaryConditions, #PersonalizedMedicine, #PhenotypeGenotypeCorrelation, #GeneIdentification, #MedicalGenetics, #Research, #Genomics

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September 25, 2024

Heart Disease Risk

The Role of Genetics in Cholesterol, Heart Disease Risk


At the 2024 Family Heart Global Summit, Helen Hobbs, MD, investigator for the Howard Hughes Medical Institute and professor of internal medicine and molecular genetics at the University of Texas Southwestern Medical Center, shared groundbreaking insights into the genetic roots of high cholesterol and offered a detailed look at how genetic discoveries are reshaping the landscape of cardiovascular disease prevention and treatment.

Her presentation centered on decades of research into familial hypercholesterolemia (FH) and cholesterol regulation, and highlighted key topics like the French Canadian deletion, low-density lipoprotein receptor (LDLR) mutations, and the implications of lifelong low LDL cholesterol levels on coronary heart disease (CHD).

The French Canadian Deletion: A Historical Genetic Anomaly

Hobbs began by recounting one of her most compelling discoveries: the French Canadian deletion. This mutation, which affects the LDLR gene, has a particularly high prevalence among French Canadians, with 63% of individuals with heterozygous FH in Quebec, Canada carrying this specific deletion.1

This mutation is a product of genetic isolation. Between 1608 and 1763, around 8000 settlers from France established themselves in what is now Quebec. Due to linguistic and geographical separation from surrounding populations, these settlers formed a genetically isolated group. Over time, the mutation that disrupts the LDL receptor—essential for clearing LDL cholesterol from the blood—became common among this population.

“We figured out that they were missing part of the gene, the part that goes to the promoter that turns the gene on in the very first part of the gene, so no protein was being made,” Hobbs explained.

She identified this specific mutation during her early research while examining the genetic profiles of people with FH, after she noticed that almost everyone in the sample with this deletion had French ancestry. This mutation provided a critical piece of the puzzle in understanding how FH manifests at a population level and underscored the role of genetic bottlenecks in amplifying certain mutations.

The Power of Low LDL: Lifelong Protection Against Heart Disease

A central theme of Hobbs’ presentation was the protective effect of lifelong low LDL levels on coronary heart disease (CHD). Drawing on data from the Dallas Heart Study, she presented compelling evidence that individuals with naturally low LDL levels due to genetic mutations are significantly less likely to develop CHD.

In her presentation, Hobbs highlighted a significant discovery related to genetic mutations in the PCSK9 gene, which plays a crucial role in cholesterol regulation. She explained that 2% of Black or African American individuals in the Dallas Heart Study carried mutations in PCSK9—a gene that promotes LDL receptor degradation—and that they had 40% lower LDL cholesterol levels compared with those without the mutation.2 These participants with the PCSK9 mutation also saw a 28% reduction in mean LDL cholesterol after using statins, leading to an astounding 88% reduction in CHD risk. A similar sequence variation was found in 3% of White participants, though the effect on LDL reduction was more modest. patients with the mutations who used statins saw a 15% reduction in LDL cholesterol and a 46% reduction in CHD risk—a smaller but still significant result.

The findings from both groups reinforced a central question in Hobbs’ research: what is the long-term effect of having low LDL cholesterol from birth on CHD risk? By identifying these genetic mutations and their effects, her team was able to draw a direct link between lifelong low LDL levels and a dramatic reduction in CHD.

Genetic Discoveries Pave the Way for Future Therapies

PCSK9 has also become a focal point in cholesterol management research, as mutations in PCSK9 can either increase or decrease its activity. In individuals with loss-of-function mutations, PCSK9 is unable to degrade LDL receptors effectively, leading to significantly lower LDL levels. PCSK9 inhibitor therapies, first approved in 2015, have been shown to reduce LDL levels by as much as 60% and significantly lower the risk of CHD events.3 More recent developments, such as the siRNA-based drug inclisiran, offer a more convenient dosing schedule, requiring only 2 injections per year. However, Hobbs acknowledged the challenges patients face in accessing these therapies due to cost and availability.

Hobbs concluded her presentation by reflecting on how genetics has transformed our understanding of cholesterol metabolism and its connection to heart disease. Her research has not only identified key mutations, but also paved the way for innovative therapies that could change the trajectory of heart disease for millions. Looking at her major discoveries in the space of cholesterol management throughout her career, it is no surprise that Hobbs was honored with the Family Heart Pioneer Award during the summit.

While she emphasized that there is still much to learn, her presentation left the audience with a sense of optimism about the future of cholesterol management. In closing, Hobbs offered a message of perseverance, particularly to women in science and medicine. Reflecting on the challenges and rewards of her own journey, she emphasized the importance of staying committed to discovery, no matter the obstacles.

“Stay in the game,” Hobbs told women everywhere, encouraging them to keep pushing boundaries and contributing to advances that will shape the future of health care.

genetics, cholesterol, heart disease, LDL cholesterol, HDL cholesterol, triglycerides, familial hypercholesterolemia, LDL receptor gene, lipid metabolism, apolipoprotein E, ApoE, cardiovascular risk, gene mutations, genetic predisposition, prevention strategies, personalized medicine, statins, diet, lifestyle changes, risk factors,

#Genetics, #Cholesterol, #HeartDisease, #LDLCholesterol, #HDLCholesterol, #Triglycerides, #FamilialHypercholesterolemia, #LDLReceptorGene, #LipidMetabolism, #ApolipoproteinE, #ApoE, #CardiovascularRisk, #GeneMutations, #GeneticPredisposition, #PreventionStrategies, #PersonalizedMedicine, #Statins, #Diet, #LifestyleChanges, #RiskFactors

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September 24, 2024

Genetic Analysis of Animals

A new genetic analysis of animals in the Wuhan market in 2019 may help find COVID-19's origin



Scientists searching for the origins of COVID-19 have zeroed in on a short list of animals that possibly helped spread it to people, an effort they hope could allow them to trace the outbreak back to its source.

Researchers analyzed genetic material gathered from the Chinese market where the first outbreak was detected and found that the most likely animals were racoon dogs, civet cats and bamboo rats. The scientists suspect infected animals were first brought to the Wuhan market in late November 2019, which then triggered the pandemic.

Michael Worobey, one of the new study's authors, said they found which sub-populations of animals might have transmitted the coronavirus to humans. That may help researchers pinpoint where the virus commonly circulates in animals, known as its natural reservoir.

"For example, with the racoon dogs, we can show that the racoon dogs that were (at the market) … were from a sub-species that circulates more in southern parts of China," said Worobey, an evolutionary biologist at the University of Arizona. Knowing that might help researchers understand where those animals came from and where they were sold. Scientists might then start sampling bats in the area, which are known to be the natural reservoirs of related coronaviruses like SARS.


While the research bolsters the case that COVID-19 emerged from animals, it does not resolve the polarized and political debate over whether the virus instead emerged from a research lab in China.

Mark Woolhouse, a professor of infectious diseases at the University of Edinburgh, said the new genetic analysis suggested that the pandemic "had its evolutionary roots in the market" and that it was very unlikely COVID-19 was infecting people before it was identified at the Huanan market.

"It's a significant finding and this does shift the dial more in favor of an animal origin," Woolhouse, who was not connected to the research, said. "But it is not conclusive."

An expert group led by the World Health Organization concluded in 2021 that the virus probably spread to humans from animals and that a lab leak was "extremely unlikely." WHO chief Tedros Adhanom Ghebreyesus later said it was "premature" to rule out a lab leak.


An AP investigation in April found the search for the COVID origins in China has gone dark after political infighting and missed opportunities by local and global health officials to narrow the possibilities.

Scientists say they may never know for sure where exactly the virus came from.

In the new study, published Thursday in the journal Cell, scientists from Europe, the U.S. and Australia analyzed data previously released by experts at the Chinese Center for Disease Control and Prevention. It included 800 samples of genetic material Chinese workers collected on Jan. 1, 2020 from the Huanan seafood market, the day after Wuhan municipal authorities first raised the alarm about an unknown respiratory virus.

Chinese scientists published the genetic sequences they found last year, but did not identify any of the animals possibly infected with the coronavirus. In the new analysis, researchers used a technique that can identify specific organisms from any mixture of genetic material collected in the environment.


Worobey said the information provides "a snapshot of what was (at the market) before the pandemic began" and that genetic analyses like theirs "helps to fill in the blanks of how the virus might have first started spreading."

Woolhouse said the new study, while significant, left some critical issues unanswered.

"There is no question COVID was circulating at that market, which was full of animals," he said. "The question that still remains is how it got there in the first place."

Wuhan market, COVID-19 origin, genetic analysis, wildlife trade, animal species, raccoon dogs, intermediary hosts, genomic data, SARS-CoV-2-like viruses, zoonotic spillover, genetic makeup, human COVID-19 cases, evolutionary lineage, viral reservoirs, wet markets, cross-species transmission, coronaviruses, epidemiological patterns, wildlife-to-human transmission, outbreak prevention.

#WuhanMarket, #COVID19Origin, #GeneticAnalysis, #WildlifeTrade, #RaccoonDogs, #IntermediaryHosts, #SARSCoV2, #ZoonoticSpillover, #GenomicData, #ViralEvolution, #AnimalSpecies, #CrossSpeciesTransmission, #PandemicOrigins, #ViralReservoirs, #Coronaviruses, #WetMarkets, #Epidemiology, #WildlifeToHuman, #OutbreakPrevention, #VirusOrigins.

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September 23, 2024

Age-Related Visual Loss

 Key mechanism behind common genetic cause of age-related visual loss discovered


Important insights into the mechanisms behind Fuchs endothelial corneal dystrophy (FECD), a common cause of age-related visual loss, have been revealed in a new study led by UCL researchers.

FECD is a common, inherited eye condition that primarily affects the cornea, the clear front part of the eye. It is one of the leading causes of vision loss as people age and is the most common reason for corneal transplants in high-income countries. FECD affects the corneal endothelial cells, which form a layer responsible for controlling fluid balance in the cornea. When these cells are lost more quickly than usual in people with FECD, the cornea becomes swollen and cloudy, leading to blurred vision.

The research, led by a team in Dr. Alice Davidson's Inherited Corneal Disease Lab at UCL Institute of Ophthalmology, has revealed how FECD progresses at a molecular level, and highlights the importance of understanding genetic instability—when cells have high frequency of mutations—in developing new treatments for FECD and diseases caused by similar genetic mutations, such as Huntington's disease and other neurological and neuromuscular diseases.

The study utilized advanced optical genome mapping with single-molecule precision where researchers found extreme levels of instability to identify how the disease progresses. These findings were exclusively in the corneal endothelial cells of individuals with FECD. The study also identified that both size and patient age influence instability rates.

Dr. Christina Zarouchlioti (UCL Institute of Ophthalmology), lead author, said, "We are excited to share these results and the impact they might have for the future of patients with FECD. We also know that the study's implications extend beyond FECD, positioning it as a valuable model for understanding a growing number of other diseases, such as Huntington's disease and myotonic dystrophies, which share similar mechanisms."

A key factor in developing FECD is the expansion of a specific DNA sequence within the TCF4 gene, called CTG18.1. This genetic change, known as a short tandem repeat expansion, has been identified as the most common risk factor for FECD across all studied populations.

Researchers are now focused on a new series of experiments to understand how this mechanism plays out throughout human development to better understand when may be the most effective time to therapeutically intervene.

Complement system, genetic mutations, macular degeneration, inflammatory responses, retina, photoreceptor cells, CFH gene, complement pathway, ARMS2 gene, HTRA1 gene, molecular pathways, age-related macular degeneration, targeted gene therapies, immunotherapies, oxidative stress, protein misfolding, chronic inflammation, retinal cell death, visual loss, genetic disease.

#ComplementSystem, #GeneticMutations, #MacularDegeneration, #Inflammation, #RetinalHealth, #PhotoreceptorCells, #CFHGene, #ComplementPathway, #ARMS2, #HTRA1, #MolecularMechanisms, #AMD, #GeneTherapy, #Immunotherapy, #OxidativeStress, #ProteinMisfolding, #ChronicInflammation, #RetinalDegeneration, #VisualLoss, #GeneticResearch

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September 21, 2024

Genetic Trait from Toddlerhood to Adolescence

Food fussiness a largely genetic trait from toddlerhood to adolescence



The study, published in the Journal of Child Psychology & Psychiatry and funded by the UK mental health charity MQ Mental Health Research, compared survey results of parents with identical or non-identical twins in England and Wales from the ages of 16 months to 13 years.

The research team found that average levels of food fussiness were relatively stable during this period, peaking somewhat around the age of seven and declining slightly after that.

They concluded that genetic differences in the population accounted for 60% of the variation in food fussiness at 16 months, rising to 74% and over between the ages of three and 13.

Environmental factors shared between twins, such as the types of foods that are eaten at home, were found to be significant only in toddlerhood, while environmental factors unique to each twin (i.e., not shared by co-twins), such as individual personal experiences (e.g., having different friends), became more influential in later years.

Food fussiness describes the tendency to eat a small range of foods, due to selectivity about textures or tastes, or reluctance to try new foods.

Lead author Dr Zeynep Nas (UCL Behavioural Science & Health) said: “Food fussiness is common among children and can be a major source of anxiety for parents and caregivers, who often blame themselves for this behaviour or are blamed by others.

“We hope our finding that fussy eating is largely innate may help to alleviate parental blame. This behaviour is not a result of parenting.

“Our study also shows that fussy eating is not necessarily just a ‘phase’, but may follow a persistent trajectory.”

Senior author Dr Clare Llewellyn (UCL Behavioural Science & Health) said: “While genetic factors are the predominant influence for food fussiness, environment also plays a supporting role.

“Shared environmental factors, such as sitting down together as a family to eat meals, may only be significant in toddlerhood. This suggests that interventions to help children eat a wider range of foods, such as repeatedly exposing children to the same foods regularly and offering a variety of fruits and vegetables, may be most effective in the very early years.”

The research team analysed data from the UCL-led Gemini study, the largest twin cohort ever set up to study genetic and environmental contributions to early growth, which involves 2,400 sets of twins.

Parents filled in questionnaires about their children’s eating behaviours when the children were 16 months, three, five, seven and 13 years old.

To disentangle genetic from environmental influences, the researchers compared the similarity in fussy eating between non-identical twin pairs, who share 50% of their genes, with the similarity between identical twin pairs, who share 100% of their genes.

They found that non-identical twin pairs were much less similar in their fussy eating than identical twin pairs, indicating a large genetic influence.

The team also found that identical twin pairs became more different to each other in their fussy eating as they got older, indicating an increase in the role of unique environmental factors at older ages. (Any differences between identical twin pairs are down to unique environmental factors, as identical twin pairs share both their genes and certain aspects of their environment that make them more similar to each other.)

Unique environmental factors accounted for about a quarter of individual differences between children in fussy eating by ages seven and 13, the researchers estimated.

Shared environmental factors, meanwhile, accounted for a quarter of individual differences between children in food fussiness at 16 months, with a negligible effect in later years.

Senior author Dr Alison Fildes (University of Leeds) said: “Although fussy eating has a strong genetic component and can extend beyond early childhood, this doesn’t mean it is fixed. Parents can continue to support their children to eat a wide variety of foods throughout childhood and into adolescence, but peers and friends might become a more important influence on children’s diets as they reach their teens.”

Among the study limitations, the researchers noted that there were fewer participants at age seven (703 children) compared to other time points and that the study sample had a large proportion of white British households of higher socio-economic backgrounds compared to the general population of England and Wales.

In future, the team said, research should focus on non-western populations where food culture, parental feeding practices and food security may be quite different.

Coxsackievirus A16, CV-A16, genotyping, phylogeography, hand foot and mouth disease, HFMD, Enterovirus A, RNA virus, genetic diversity, molecular epidemiology, sub-genotypes, viral evolution, transmission patterns, outbreak control, public health, vaccine development, RNA sequencing, phylogenetics, viral spread, global health

 #CoxsackievirusA16, #Genotyping, #Phylogeography, #HandFootMouthDisease, #HFMD, #EnterovirusA, #GeneticDiversity, #MolecularEpidemiology, #SubGenotypes, #ViralEvolution, #TransmissionPatterns, #OutbreakControl, #PublicHealth, #VaccineDevelopment, #RNASequencing, #Phylogenetics, #ViralSpread, #GlobalHealth, #VirusResearch, #Epidemiology

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September 20, 2024

Syphilis genetics

Searching for a vaccine against an ancient scourge: Syphilis genetics study points to a potential target


Syphilis cases have surged worldwide, leaving public health officials scrounging for ways to stop the spread. Now, a large, collaborative study of syphilis genetics from four continents has found hints of a possible target for a vaccine.

Syphilis is a sexually transmitted illness that first appeared in Europe about 500 years ago. Its initial symptoms can vary, but the spiral shaped bacterium that causes it can persist in the body for years, often in the central nervous system, and cause birth defects when it infects infants in utero. Syphilis cases decreased in the middle 20th century as easy, effective treatment with injectable penicillin became available, and became uncommon in the 1990s due to changes in sexual behavior in the wake of the HIV epidemic.

But recently, syphilis has made an unwelcome comeback. There were 207,255 cases in the U.S. in 2022, according to the Centers for Disease Control (CDC), more than any time since the 1950s. Babies, some of them stillborn, made up 3,755 of those cases. Other countries worldwide are seeing the same disturbing upward trend.

Stopping syphilis's spread has become a pressing public health goal. Now, an international collaboration of researchers and doctors has collected one of the most extensive genomic surveys of the syphilis bacterium to date and correlated the genetic data with clinical information about the patients who provided the samples. They are using the data to search for proteins on the surface of the microbe that don't vary. Such stable proteins could be good targets for a vaccine.

#Syphilis, #TreponemaPallidum, #VaccineDevelopment, #OuterMembraneProteins, #ImmuneEvasion, #InfectionProcess, #PublicHealth, #AntibioticResistance, #TransmissionPatterns, #Pathogenesis, #ImmuneResponse, #VaccineTarget, #BacterialEvolution, #GlobalHealth, #InfectiousDisease, #PreventativeStrategies, #Antibiotics, #VaccineResearch, #SyphilisVaccine, #HealthInnovation

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September 16, 2024

Cancer Risk

Why some women enter menopause early — and how that could affect their cancer risk


Two studies of more than 100,000 women have revealed a suite of genes that help to regulate when a person enters menopause and thus the length of their reproductive span. Some of the genes could also influence the risk of cancer.

Age at menopause can vary widely and is known to be influenced by both environmental and genetic factors. The hope is that these genetic catalogues will help researchers to develop treatments for infertility and create methods for predicting when a person will enter menopause. The studies were published in Nature on 11 September1 and in Nature Genetics on 27 August2.

Rare but powerful

These studies join a bevy of recent efforts to identify genes that contribute to premature menopause. But most of those studies looked for genetic variants that are common in the population, whereas the new projects instead focused on DNA sequences that are rare but which might have a greater effect on ovarian ageing than more-common sequences do.

Hunting for rare genetic variants requires data from a large group of people. To obtain such data, geneticist Anna Murray at the University of Exeter Medical School, UK, a co-author of the Nature paper, and her colleagues relied on the UK Biobank, a massive collection of biomedical data that includes DNA-sequence data as well as information about participants’ lifestyle and health. The researchers focused on protein-coding DNA and found nine genetic variants that are associated with age at menopause. Five of the genes had not been linked to ageing of the ovaries previously.

Women with certain variants in a gene called ZNF518A, for example, were more likely to start menstruating later and undergo menopause earlier than women who did not have those forms of the gene. The result was a reproductive lifespan that was, on average, more than six years shorter.

Mutations for menopause

One factor that could trigger that early menopause is the accumulation of DNA mutations in a person’s eggs. Such mutations can trigger the repair of the eggs’ DNA — or they can cause the eggs to self-destruct. The eggs’ response to DNA damage is key in determining egg number, says Murray. “And it’s egg number that determines your reproductive lifespan.”

Mutations can also increase cancer risk, and variants in four of the genes that the team uncovered were linked not only to early menopause but also to a higher risk of cancer.

To look at the relationship between the accumulation of DNA mutations and ovarian ageing, Murray and her colleagues analysed the genetic sequences of more than 8,000 genetic ‘trios’, that of a mother, father and child.

The team found that women who carried common DNA variants that previous research had associated with earlier age at menopause were more likely to pass mutations that had arisen in their eggs to their offspring.

The finding supports the idea that DNA damage is related to ovarian ageing, says Murray. But when the team attempted to repeat their experiment using data from a different biobank, the results were no longer statistically significant.

Even so, the possible links between age at menopause and cancer are important to explore, says Kári Stefánsson, a geneticist and chief executive of the biopharmaceutical company deCODE Genetics in Reykjavik and a co-author on the Nature study. “It focuses the attention on finding a way to deal with conditions like early menopause, and the impact that it has on biology,” he says.

Infertility treatment

In the Nature Genetics study, Stefánsson and his colleagues looked for genetic variants that are linked to early menopause, focusing on variants that had that effect only if they were present in both copies of a woman’s DNA. Their search uncovered a link between age at menopause and a gene called CCDC201, which is known to be active only in immature egg cells2.

Women with certain variants of that gene underwent menopause nine years early on average. The large size of that effect and the specificity of CCDC201 activity suggests that the gene might prove to be a useful target for preventing or treating some cases of infertility, says Goriely. Such an intervention would have to be carefully designed to avoid raising the risk that it would allow eggs to transmit excess damaged DNA to children, but eggs generally contribute many fewer mutations than sperm do anyway, she notes.

“You don’t die of infertility, but for many women who suffer from it, it really is a catastrophe,” Goriely says. “We ought to do something for these women.”

“They are rare, but typically they are impactful,” says Anne Goriely, a geneticist at the University of Oxford, UK, who was not an author of the papers. “New treatments and conceptual advances often come from these rare disorders.”

#EarlyMenopause, #CancerRisk, #Estrogen, #BreastCancer, #OvarianCancer, #Genetics, #AutoimmuneDisorders, #PrematureOvarianFailure, #Smoking, #LifestyleFactors, #Chemotherapy, #RadiationTherapy, #HormoneReplacementTherapy, #Osteoporosis, #HeartDisease, #ReproductiveHealth, #MenopauseAwareness, #CancerPrevention, #HormoneHealth, #WomenHealth

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September 14, 2024

Genetics role in ovarian cancer

The Medical Minute: Genetics play big role in ovarian cancer



In 2024, about 19,680 women in the United States will receive a new diagnosis of ovarian cancer and 12,740 women will die from the disease, said Dr. Shaina Bruce, a gynecologic oncologist at Penn State Cancer Institute. The median age of all patients who develop ovarian cancer is 63.

Historically, women at increased risk for ovarian cancer are recommended to have their fallopian tubes and ovaries removed when they have completed having children. Taking that step to protect themselves comes at a heavy price ― surgical menopause.

But Bruce said medical science is catching up with ovarian cancer. Studies could lead to new methods for preventative care and the surgery needed to lower risk may be easier than it once was. Below, during Gynecologic Cancer Awareness Month, Bruce discusses the disease and why acting to reduce your risk is worth it.

What’s the connection between heredity and ovarian cancer?

About 25% of all cases of ovarian cancer occur in people who have a hereditary predisposition for the disease, Bruce said, so if one of your first degree (mother or sister) or second degree (aunt or first cousin) relatives have had the disease, you should undergo genetic testing to see if you are also at increased risk.

The most common genetic culprits of ovarian cancer are mutations on BRCA1 and BRCA2, two genes also known to also increase the risk for breast, prostate and other kinds of cancer. A patient with a mutation on their BRCA1 gene has a 40% likelihood of developing ovarian cancer, Bruce said, and BRCA2, 20%.

In patients with a known genetic mutation that increases risk of certain cancers, steps may be taken to reduce their risk. Family members also can determine whether they have the same genetic risk.

What does the surgery entail?

“The trouble with removing ovaries in a young woman in her 30s and 40s is that it puts the patient into surgical menopause,” Bruce said. Women who receive the surgery have the same symptoms of menopause a woman might experience without surgery but later in life ― hot flashes, vaginal dryness and mood changes.

“Also, the estrogen that your ovaries make is important,” Bruce said. The hormone protects a woman’s heart and bones, and can decrease her odds of one day developing dementia.

Within the past 10 to 15 years, however, doctors have discovered that more than 80% of ovarian cancers begin in the fallopian tubes. Penn State College of Medicine is joining a surgical choice study that will compare removing only the fallopian tubes of women with a mutation on the BRCA1 gene ― with a plan to remove the ovaries over later on ― to women who have had both the tubes and ovaries removed. Researchers hope to determine effects of both practices on their risk of developing ovarian cancer. Women who have a BRCA1 mutation and are interested in participating in this study should contact Penn State Health Gynecologic Oncology for more information.

One thing you can do to decrease your risk if you’re planning tubal ligation surgery ― or “having your tubes tied” ― rather than burning or surgically tying off the fallopian tubes, is asking to have the tubes removed altogether.

In any case, the surgery ― whether it’s removing just the fallopian tubes or the ovaries and tubes ― is minimally invasive outpatient surgery. It’s three small incisions and usually takes a couple of weeks to recover.

Are there any non-surgical possibilities for mitigating your risk?

Some women opt to wait to have the surgery until after they have finished having children. Screening for ovarian cancer regularly with transvaginal ultrasounds and a blood test to look for cancer indicating antigen is also an option. That’s often recommended in young patients, Bruce said.

For BRCA1 patients, doctors usually don’t recommend surgery until age 35 to 40. The recommended age for preventative surgery for BRCA2 patients is 40 to 45.

“If a patient is younger than that, we can safely do screening until they’re ready for risk reducing surgery,” Bruce said.

Are the BRCA1 and BRCA2 mutations risky for men as well?

Yes, men can also develop breast cancer and the mutation can also play a role in the risk of prostate cancer, pancreatic cancer and melanoma, Bruce said. So, if a female family member has a known BRCA mutation, male relatives should also get checked.

Who should get checked?

Anyone who has a first- or second-degree relative who was affected by ovarian cancer meets the criteria for testing. In someone with no family members with ovarian cancer, their lifetime risk is 1% to 2%. If the patient has one first degree relative who has been affected by ovarian cancer, their lifetime risk is about 5%. Two relatives, 7% to 10%.

At the moment, doctors don’t screen the people for ovarian cancer unless they have a genetic predisposition for it.

What other risk factors are there besides heredity for ovarian cancer?

Using hormone replacement therapy after menopause. Never having been pregnant. Endometriosis

The idea of preventative surgery sounds awful. What if I don’t want to know?

Compared with the surgery to remove ovarian cancer itself, preventative surgery is usually worth it, Bruce said.

“Ignorance is bliss, right?” Bruce said. “Unfortunately, in oncology I hear that more often than I’d like to admit. But I would say knowledge is power. If you know you have a predisposition, often there’s something that can be done about it. Usually, what can be done preventatively or to reduce your risk is less invasive than what would need to be done if you were diagnosed with the cancer in question.”

ovarian cancer, genetics, BRCA1, BRCA2, hereditary cancer, HBOC, Lynch syndrome, genetic mutations, family history, genetic testing, genetic counseling, early detection, preventive measures, targeted therapies, PARP inhibitors, personalized treatment, risk factors, gynecologic malignancy, cancer research, gene mutations,

#OvarianCancer, #Genetics, #BRCA1, #BRCA2, #HereditaryCancer, #HBOC, #LynchSyndrome, #GeneticMutations, #FamilyHistory, #GeneticTesting, #GeneticCounseling, #EarlyDetection, #PreventiveMeasures, #TargetedTherapies, #PARPInhibitors, #PersonalizedTreatment, #RiskFactors, #CancerResearch, #GynecologicCancer, #GeneMutations

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