Delivering genetic material with MOFs for new therapies

In biomedicine, metal-organic frameworks can be used to deliver pharmaceuticals around the human body. A KAUST-led team has developed a MOF-based system for getting DNA across cell membranes into target cells.

by  King Abdullah University of Science and Technology

An emerging type of material called a metal-organic framework (MOF) could help improve the delivery of genetic material for treating disease.

MOFs are hybrid materials constructed from metal ions linked by organic molecules. In biomedicine, they have mostly been used as delivery vehicles for small-molecule pharmaceuticals, but now a KAUST-led team has developed a MOF-based system for getting DNA across cell membranes into target cells.

The researchers built their MOFs using a collection of nucleic acid and unnatural amino acid building blocks tethered together by zinc atoms, assembled in a pyramid-like array. They loaded up the resulting materials with single-stranded DNA. The structures protected the genetic cargo from enzymatic degradation and helped ferry the single-stranded DNA into cells, where it ended up inside the nucleus—the cell’s inner sanctum where all gene activity takes place.

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Stanford University uses AI computing to cut DNA sequencing down to five hours

Speeding up the genome sequencing process has earned the project a Guinness World Record title.

By Aimee Chanthadavong

A Stanford University-led research team has set a new Guinness World Record for the fastest DNA sequencing technique using AI computing to accelerate workflow speed. 

The research, led by Dr Euan Ashley, professor of medicine, genetics and biomedical data science at Stanford School of Medicine, in collaboration with Nvidia, Oxford Nanopore Technologies, Google, Baylor College of Medicine, and the University of California, achieved sequencing in just five hours and two minutes. 

The study, published in The New England Journal of Medicine, involved speeding up every step of genome sequencing workflow by relying on new technology. This included using nanopore sequencing on Oxford Nanopore’s PromethION Flow Cells to generate more than 100 gigabases of data per hour, and Nvidia GPUs on Google Cloud to speed up the base calling and variant calling processes. 

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Rapid DNA Sequencing Promises Timely Diagnosis for Thousands of Rare Diseases

For children suffering from rare diseases, it usually takes years to receive a diagnosis. This “diagnostic odyssey” is filled with multiple referrals and a barrage of tests, seeking to uncover the root cause behind mysterious and debilitating symptoms.

A new speed record in DNA sequencing may soon help families more quickly find answers to difficult and life-altering questions.

In just 7 hours, 18 minutes, a team of researchers at Stanford Medicine went from collecting a blood sample to offering a disease diagnosis. This unprecedented turnaround time is the result of ultra-rapid DNA sequencing technology paired with massive cloud storage and computing. This improved method of diagnosing diseases allows researchers to discover previously undocumented sources of genetic diseases, shining new light on the 6 billion letters in the human genome.

More than 7,000 rare diseases affect 300 million people worldwide, 50% of whom are children. Of these diseases, 80% have a genetic component. The onset of some rare genetic diseases can be swift and debilitating. Spotting symptoms and identifying the root cause is a race against the clock for many families.

I’m a biotechnology and policy scholar who works on improving access to innovative health care technologies. Whether it’s simple and affordable tests or sophisticated and expensive gene therapies, medical breakthroughs need to reach populations around the world. I believe that ultra-rapid DNA sequencing is key to casting a wider net and providing a faster turnaround for diagnosing rare diseases.

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Scientists Develop World’s Smallest ‘easy-to-use’ Antenna Using Human DNA

Calling it an ‘easy-to-use device’, the scientists said that this nanoantenna will help scientists identify new drugs and better understand nanotechnologies.

By Harsh Vardhan 

A team of chemists from the University of Montreal has designed the world’s smallest antenna using human DNA, which is the building block of genetic material and measures 20,000 times smaller than a human hair. Calling it an ‘easy-to-use device’, the scientists said that this nanoantenna will help scientists identify new drugs and better understand natural and human-designed nanotechnologies. Fitted with fluorescent molecules at the end, this nanoantenna has basically been designed to monitor the motions of proteins. Professor Alexis Vallée-Bélisle, who is also the study’s senior author said as per the University’s official release.

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New method for genetic analysis of resting human immune cells

by  Ludwig Maximilian University of Munich

CD4+ T cells are important parts of the immune system and play a key role in defending the body against pathogens. As they possess a great variety of defense mechanisms against HIV in their resting state, they are infected only very rarely—but these few infected cells form a latent reservoir for HIV in the body that currently cannot be reached by antiviral drugs. Consequently, the virus can spread again from there after activation of the CD4+ T cells. Understanding how HIV interacts with resting CD4+ T cells is essential for finding new therapeutic approaches. Scientists led by Prof. Oliver T. Keppler from the Max von Pettenkofer Institute at LMU have now developed a method that for the first time allows these specific immune cells to be genetically manipulated under physiological conditions in an efficient and uncomplicated manner. As the authors report in the journal Nature Methods, this permits previously unobtainable insights into the biology of these cells.

Resting CD4+ T cells had been scarcely amenable to genetic manipulations, because the available methods generally presuppose dividing cells, as Keppler explains. “And resting cells do not divide by definition.” As the first step in the development of the new method, the team of scientists optimized the cultivation conditions. As a result, the researchers were able to keep these cells alive in the laboratory after extracting them from the blood of healthy donors not just for 3-4 days as before, but for up to six weeks. The decisive progress came with an advance in nucleofection, a special method that allows reagents to be delivered into the nucleus of a cell. Using this technique, the researchers introduced the genetic scissors CRISPR-Cas into resting CD4+ T cells, enabling them to make targeted modifications to the genome of the host cells—for example, by eliminating genes by means of so-called knockouts. “This combination worked very efficiently, and we were able to reach and genetically manipulate around 98 percent of the cells. Moreover, we did this without activating the CD4+ T cells,” says Keppler. “What was particularly exciting was that we were able to eliminate up to six genes simultaneously with high efficiency by means of a single nucleofection. Nobody had managed to do that in primary cells before—and we did it with cells isolated from an intact organ.”

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Researchers use genetics to develop model for personalized diets

By Andria Kades

23 Dec 2021 — Researchers at the University of Copenhagen are developing a personalized dietary profile that can tell individuals what is good and bad for them to eat, depending on their health status.

The researchers at the Food Science department expect their project to be applicable for people suffering from asthma, as well as a range of inflammatory diseases such as multiple sclerosis and rheumatoid arthritis. If successful, the method could be used in the health care system. 

“Instead of treating diseases, we will be able to move toward the treatment of individuals by changing the largest environmental factor, namely the diet,” lead researcher on the project, associated professor Morten Arendt Rasmussen, tells NutritionInsight.

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New Gene-Writing Tool Helps To Develop Advanced Gene Therapies

Original story from Pompeu Fabra University Barcelona 

An international, multidisciplinary team of researchers from the Translational Synthetic Biology Laboratory at Pompeu Fabra University (Barcelona, Spain), led by Dr. Marc Güell, has published an article in the scientific journal Nature Communications showing the potential of Find Cut-and-Transfer (FiCAT) technology as a state-of-the-art tool for gene writing to develop advanced therapies that are safer and more effective in their future clinical application in patients with genetic and oncological diseases that have few treatment options.

The UPF Translational Synthetic Biology Laboratory has been working on gene editing and synthetic biology applied to gene therapies since 2017. FiCAT technology is an important scientific breakthrough to overcome the current limitations of the technology used today for genome editing and gene therapy.

“Human genome engineering has significantly progressed in the last decade with the development of new editing tools, but there was still a technology gap that would allow therapeutic genes to be transferred efficiently with few size limitations”, comments Dr. Marc Güell, supervisor of the study.

In this work, the researchers develop an efficient and precise programmable gene writing technology based on the combination of modified proteins CRISPR-cas and piggy Bac transposase (PB), succeeding in inserting small and large fragments. Dr. Maria Pallarès, co-first author of the study explains that: “CRISPR stands out for its precision when editing small fragments. However, transposases allow us to insert large fragments but in an uncontrolled manner. We have combined the best of each technology”.

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$17 million will launch trial of CRISPR cure for sickle cell disease

Mark Walters of UCSF Benioff Children’s Hospital Oakland explains how a CRISPR cure for sickle cell disease would benefit patients.

By Robert Sanders

A small clinical trial of a CRISPR cure for sickle cell disease, approved earlier this year by the U.S. Food and Drug Administration, has received $17 million to enroll about nine patients, the first of which may be selected before the end of the year.

The funds — $8.4 million from the California Institute for Regenerative Medicine (CIRM) and $8.6 million from the National Heart, Lung, and Blood Institute (NHLBI) — were awarded to UCSF Benioff Children’s Hospital Oakland, which will coordinate the four-year clinical study in collaboration with colleagues at the University of California, Berkeley, and UCLA.

The trial will be among the first to apply CRISPR-Cas9 gene editing technology in humans to snip out the mutated beta-globin gene that causes the disease and replace it with the correct version, which should cure the patient and prevent the painful symptoms and early death that accompany the disease.

This will be the only trial to deliver the Cas9 enzyme and the correct beta-globin gene into a patient’s stem cells without using a virus. The therapy, referred to as CRISPR_SCD001, involves inserting the beta-globin gene and Cas9 enzyme into stem cells via electroporation after the cells have been removed from the patient’s bone marrow. The corrected stem cells are then reinfused to multiply and repopulate the patient’s bone marrow.

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How Genetic Testing Will Create Personalized Therapeutics for Rare Diseases

“Personalized medicine represents a better paradigm in medicine than one-size-fits-all, trial-and-error, which is what most medicine is.”

By Audrey Carleton

For patients with rare symptoms, landing on a course of treatment often comes only after a long, winding road of doctor’s visits, consultations, lab work and experiments. It’s costly, emotionally turbulent, and tiresome.

It’s what many in the world of medicine call the “diagnostic odyssey,” referring to the time it takes from the initial onset of symptoms to final diagnosis. And it’s a path that, for the average patient, takes about 8 years.

“You go from doctor to doctor for years and years, and you don’t figure out what’s going on,” Edward Abraham, founder of the Personalized Medicine Coalition (PMC), an education and advocacy group, told Motherboard. “All of that is expensive.” 

It’s a cycle Abraham’s group, which consists of both non- and for-profit organizations from across the healthcare industry, is striving to do away with. Their solution? Improving access to genetic testing to allow for the creation of personalized therapeutics. 

The traditional approach to medicine, Abraham describes, is one-size-fits-all. When a patient presents a rare, difficult-to-diagnose symptom, their healthcare provider may try a slew of treatments with varying effectiveness, all of which have been developed to treat the largest number of patients at once, rather than to suit the needs of a specific individual.

With personalized medicine, hard-to-diagnose symptoms are inspected by going straight to the source — the human genome. With genetic sequencing, a sample of a patient’s DNA is taken through blood, skin, or tissue, for example. Then, their entire genetic code, all 3.2-billion base pairs, are analyzed for signs of mutations that may be causing a symptom or underlying disorder. With this information, a doctor is better equipped to search for a personalized treatment for an individual disorder, or to create one from scratch. 

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Firm raises $15m to bring back woolly mammoth from extinction

The remains of a well-preserved baby mammoth, named Lyuba, displayed in Hong Kong in 2012. 

By Ian Sample

Scientists set initial sights on creating elephant-mammoth hybrid, with first calves expected in six years.

Ten thousand years after woolly mammoths vanished from the face of the Earth, scientists are embarking on an ambitious project to bring the beasts back to the Arctic tundra.

The prospect of recreating mammoths and returning them to the wild has been discussed – seriously at times – for more than a decade, but on Monday researchers announced fresh funding they believe could make their dream a reality.

The boost comes in the form of $15m (£11m) raised by the bioscience and genetics company Colossal, co-founded by Ben Lamm, a tech and software entrepreneur, and George Church, a professor of genetics at Harvard Medical School who has pioneered new approaches to gene editing.

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CRISPR gene editing technology is revolutionizing healthcare as we know it. 

The technology, which earned two of its discoverers a Nobel Prize in 2020, can target and edit genes more easily and more precisely than its predecessors. 

Yet as promising as CRISPR has been over the past several years, it’s mostly been developed in the lab.

Thankfully, that is now changing as a growing number of clinical trials are beginning to test gene therapies in humans. 

Early CRISPR trials have focused on hereditary blindness and diseases of the blood, including cancer and sickle cell anemia.  

The problem is that although cutting-edge, these therapies can be costly and intense. For example, in one trial for sickle cell anemia, doctors remove cells from the body, edit them in a dish, and then infuse them back into the patient.

Such a complicated approach won’t work as readily for other diseases. 

What we need is a general delivery method for CRISPR, so that it can be used like any other medication. 

And a recent clinical trial run by researchers at University College London (UCL) has made a key, promising step in that direction. Discussing the latest developments in biotech—using biology astechnology—is a key focus of my year-round coaching program Abundance360.


Cracking one more layer of genetic code will finally enable personalized medicine, researcher says

The New Scientist

By McMaster University

When the Human Genome Project reached its ambitious goal of mapping the entire human genome, it seemed the world was entering an era of personalized medicine, where evidence from our own specific genetic material would guide our care.

That was 2003, and nearly a generation after that spectacular collaborative achievement, we are still waiting for that promise to materialize. We may know that a person carries a gene associated with breast cancer, for example, but not whether that person will go on to develop the disease.

New research by McMaster University evolutionary biologist Rama Singh suggests the reason is that there is another, hidden layer that controls how genes interact, and how the many billions of possible combinations produce certain results. That layer is composed of largely uncharted biochemical pathways that control gene expression in cells through chemical reactions.

Continue reading… “Cracking one more layer of genetic code will finally enable personalized medicine, researcher says”