AI tool reveals DNA exists in partially open states

                    

    Scientists from the Gladstone Institutes and Arc Institute used artificial intelligence to discover that DNA is often stored in partially open states, rather than being fully closed or fully accessible as previously believed.

    DNA is wrapped around protein structures called nucleosomes, which help package over six feet of DNA inside each cell. For years, researchers thought genes were either “on” or “off” depending on whether DNA was tightly wrapped. However, this study found the genome behaves more like a volume dial, allowing different levels of gene activity.

    Using an AI tool called IDLI, researchers identified 14 distinct nucleosome structural states. More than 85% of nucleosomes showed some distortion, meaning sections of DNA were partially exposed and potentially available for gene regulation. This creates a more flexible system for controlling how genes function.

    These findings are important in genetics because subtle gene expression changes are linked to diseases like cancer, aging, and neurodegenerative disorders. Understanding this hidden DNA “grammar” could help scientists design future treatments that adjust gene activity more precisely.

Article Link: https://www.drugtargetreview.com/ai-tool-reveals-dna-exists-in-partially-open-states/2135350.article

Additional Resource: https://distilinfo.com/2026/04/30/ai-reveals-dna-is-far-more-accessible/

Baby Is Healed With World’s First Personalized Gene-Editing Treatment

            

           A 9 ½ month baby, KJ Muldoon, now became the first human ever to receive a personalized gene-editing treatment. The baby was born with CPS1 deficiency, which is an uncommon genetic disorder with 1-1.3 million births that prevents the body from removing ammonia. Usually, a baby is born with this disorder and passes away within a week, and even survivors remain with severe brain damage and often require a liver transplant. 

                                                            CRISPR gene editing.

        Luckily for this specific baby, doctors at the Children’s Hospital of Philadelphia and research from the University of Pennsylvania discovered a custom CRISPR-based “base editing” therapy for KJ’s exact genetic mutation. The treatment involves using lipid nanoparticles to deliver the editor to the liver. It also contains instructions to produce an enzyme that fixes the mutated DNA letter. It also includes a “GPS” that targets KJ’s unique mutation. This specific process is much faster and cheaper than gene therapy before.

This is a huge development for the healthcare community. This can impact over 30 million Americans and over 7,000 rare genetic disorders. Whereas previous genetic treatments offered limited hope because of the disorders being far too rare, this case offers a sense of relief because personalized gene editing could now be possible for many more patients.

KJ ultimately received three infusions of the gene editor. After the first dose, he was able to tolerate normal protein levels. His ammonia-removal medication was reduced by half. He was able to fight off viral infections that previously would have threatened his life. He is now meeting milestones of development and preparing to go home.

References

Cleveland Clinic. (2023, April 25). CRISPR gene editing 101. https://health.clevelandclinic.org/crispr-gene-editing

Kolata, G. (n.d.). Baby is healed with world’s first personalized gene-editing treatment - The New York Times. https://www.nytimes.com/2025/05/15/health/gene-editing-personalized-rare-disorders.html

Horse Discovery Leads to Hope for Humans

 A new genetic discovery within horses may open the door to many new medical advancements, and may provide new treatments for cystic fibrosis and many more inherited diseases. Horses with improves stamina have adapted to overcome a mutation in the KEAP1 protein structure. KEAP1 is part of a pathway alone with NRF2 that exists in all vertebrates and plays a role in protecting the bodies cells from oxidative stress. This pathway is also critical in metabolism. The mutation in the KEAP1 protein leads to a premature STOP codon. 

What surprised the researchers is that the horses have figured out a way to work around this STOP codon. The cells have evolved to be able to recode the signal, and allow for full translation of the gene. This is the first time this kind of skill has been seen outside of viruses, which need to alter cell DNA in order to replicate itself. What a discovery! This opens the doors for more ideas on how this can be used for treatments of diseases that are caused by a premature STOP codon. 

This evolved trait also shows that it makes the KEAP1 protein much more efficient, boosting NRF2 and allowing for more endurance and stamina during intense physical activity, and protecting the cells from reactive oxygen species. This means that this mutation may also help aid in treating age related diseases. 

Article

Viruses exhibiting similar process

Using CRISPR to Treat Patients Affected by Hereditary Angioedema

 

    In a recent article written in the Guardian, written by Ian Sample, he describes a groundbreaking new treatment that utilizes CRISPR gene editing to help patients effected by hereditary angioedema. Hereditary angioedema, also known as  HME, is a rare disease that effects roughly 50,000 people. It is caused by a mutation in the C1 inhibitor gene which causes an overproduction of the protein kallikrein. This in turn causes a build up of the protein bradykinin which is responsible for leaky blood vessels and swelling. This swelling can be life altering and potentially life threatening. 

    The article describes medical trials done by Dr. Hilary Longhurst at the University of Auckland. These trials were extremely successful. After undergoing a single dose of this permanent gene therapy many patients were able to come off long term medication which often come with many side effects while being less effective. Scientists utilized CRISPR to create "nanolipids" which were administered to patients. These "nanolipids" enter liver cells and prevent the kallikrein gene from over producing bradykinin which stops swelling.

    Despite the success of this ground breaking treatment, there is one major downside. One-shot genetic treatments range in price from 1 million to 2 million dollars. This makes treatment extremely exclusive to wealthy patients and countries.

    In my opinion this article is important because it describes the possibility of curing an extremely debilitating disease. Despite the high cost, I am hopeful that continued research and adoption of genetic medical procedures will make these treatments more accessible to everyday people.

Black Death Genes and Increasing Autoimmune Disorders

FOOD FOR THOUGHT:

 Genes that once protected our bodies during the Black Death, may now be increasing autoimmune disorders...

    An article from Harvard Medical School (HMS) details how genes that once protected our bodies during the Black Death in the 14th century, may now be increasing the prevalence of autoimmune diseases. Researchers have extracted the DNA of people who died during the time of the Black Death, and are using that to compare against the DNA of those who have lived through the COVID-19 pandemic (our time). From this data, they were able to deduce the fact that survivors of each pandemic carried genes that made them immune to the disease. This makes sense, considering the "survival of the fittest" philosophy introduced by Darwin, and due to evolutionary circumstances, it would make sense that those who survived one instance of a deadly disease could presumably survive another. The bacterium Yersinia pestis was known to cause the Black Death as it spread from animals to humans, and plays a role now, centuries later. The relevance comes into play with autoimmune disorders: those alive during our time with autoimmune diseases are more likely to carry those same infection-fighting genes that helped people survive the Black Death -- crazy right?

    This was a very fascinating article and it is interesting to see how the genes have been passed on evolutionarily through time. Not only that, but the human body has me awestruck. The things that it is capable of, such as passing on these genes that can prevent disease is so interesting to me. Furthermore, as someone with an autoimmune disease, I can't help but to wonder if I carry these same genes as well. I think it would be really fascinating to have my DNA extracted and compared to that of someone who survived the time of the Black Death, that way I could truly see if I am impacted by this phenomena. Selective pressures and immunity are quite interesting to me and I could see myself taking a deeper look into this topic in the future!

LINKS:

1. https://www.health.harvard.edu/blog/genes-protective-during-the-black-death-may-now-be-increasing-autoimmune-disorders-202212012859 

2. https://www.nature.com/articles/s41586-022-05349-x

Can gene expression predict if a brain tumor is likely to grow back?

 

Researchers from UC San Francisco and Northwestern Medicine have discovered a new accurate method to predict the best treatment for individuals with meningioma with the help of 10 other medical centers. The study shows that screening tumors based on gene expression patterns can change the course of treatment for nearly 1 in 3 people with meningioma. Meningioma is a common brain tumor that affects around 42,000 people in America annually. It is more likely to affect groups of females more than males and elderly patients. It is typically treated with either surgery or radiation depending on what number scale it is on and how severe the tumor is. The new gene expression test indicates that only 1 in 5 patients with low-grade tumors may require radiation, while approximately 2 in 5 with higher-grade tumors may benefit more from avoiding radiation. With the help of the test, researchers could see which gene was active and deactivated and discovered a set of 34 genes whose expression patterns could predict the likelihood of tumor recurrence. 

The discoveries made by this study were exciting as they paved the way for new improvements. The second link also provides more information supporting the first study. Medicine is more effective when it is targeted toward a specific individual’s needs. I hope more treatments are made in the future that are targeted towards one’s needs. The studies from this research help eliminate the guesswork in patients' treatment decisions. The studies are still ongoing, and they are trying to gather more data that can help provide more personalized care in the future. 

Links -

Can gene expression predict if a brain tumor is likely to grow back? | ScienceDaily

Can Gene Expression Predict if a Brain Tumor Is Likely to Grow Back? | UC San Francisco (ucsf.edu)

How male mosquitoes compensate for having only one X chromosome

 How male mosquitoes compensate for having only one X chromosome

    Dr. Claudia Keller Valsecchi's research team at IMB in Mainz discovered the master regulator, SOA, responsible for balancing X chromosome gene expression in male mosquitoes. This understanding is crucial for equalizing gene expression between male and female mosquitoes, which might lead to new malaria prevention strategies. Only female mosquitoes spread malaria, making understanding the molecular differences between mosquito genders essential. The study found that SOA binds to X chromosome genes, increasing their expression in males, while females produce a non-functional version.

The groundbreaking research led by Dr. Claudia Keller Valsecchi's team at IMB in Mainz is truly commendable and shows how research on small organisms like mosquito genetics can be applied to humans. Discovering the role of the SOA protein in balancing X chromosome gene expression opens the door to a deeper understanding of mosquito biology. Targeting the molecular differences between mosquito sexes could revolutionize our approach to combating this deadly disease. In the second article, Omar Akbari and his team at the University of California are using CRISPR genetic engineering to combat mosquito-borne diseases. They've developed techniques that either block viral transmission in mosquitoes or cause mosquito lethality. A notable approach being explored is pgSIT, which makes the mosquitoes sterile, preventing the need for insecticides in population control.

Links: 

https://www.sciencedaily.com/releases/2023/10/231006104515.htm

https://www.the-scientist.com/news-opinion/combating-mosquito-borne-diseases-with-crispr-70607

Prion Disease

Prion diseases are complicated and often fatal illnesses. This specific prion disease is known as kuru, or the cannibalism disorder. Although extremely rare, it is devastating, and resistance may be attainable. People with a mutation on codon 129 of the prion protein seem to be less susceptible to prion diseases if they have one or two copies. When tested on mice, it was found that a different codon, codon 127, made mice completely resistant when it was mutated. The research shows the reason behind this is because the mutation on codon 127 prevents the prion protein from becoming misshapen, which is what causes the disease.
Researchers are currently working on determining the structure of the mutated protein, and trying to use it as a defence in other diseases. I hope it is successful.



original link: https://www.nature.com/news/genetic-mutation-blocks-prion-disease-1.17725
related link: https://www.nature.com/articles/gim201032

Cure for the Common Cold?

A protein that is inside of humans is used by many viruses to replicate. In research on mice and human cells where this protein is lacking, viruses could not replicate. Researchers at Stanford University used CRISPER to deleted chunks of DNA, each missing a gene, so they can no longer make a specific protein. These chunks of genes were infected with viruses and studied to determine which proteins were interacting with viral proteins. The one protein that repeatedly interacted was SETD3, which was previously known as an actin protein helping muscles contract. Engineered Mice and human lung cells made to lack the SETD3 gene did not get sick when infected with viruses. To further surprise, this gene could also affect getting sick from diseases other than the common cold. With this new knowledge drugs can be synthesised to block the human protein and the viral from interacting, but complicated targeted treatments like this are not going to be available for prescriptions any time soon. Even so, it is always nice to know the expansion of science is working to make life better for those who are sick. I hope some form of treatment becomes available, and they are able to find cures for as many viruses that respond to the SETD3 protein as possible.

original link: https://www.sciencenews.org/article/common-cold-virus-disable-protein
related link: https://www.contagionlive.com/news/disabling-setd3-gene-could-halt-viral-infections