AI Tools Can Predict DNA Structure and Regulation

Predicted 3D structure for a segment of human genomic DNA.

Newly developed artificial intelligence (AI) programs accurately predicted the role of DNA’s regulatory elements and three-dimensional (3D) structure based solely on its raw sequence, according to two recent studies in Nature Genetics. These tools could eventually shed new light on how genetic mutations lead to disease and could lead to new understanding of how genetic sequence influences the spatial organization and function of chromosomal DNA in the nucleus, said study author Jian Zhou, Ph.D., Assistant Professor in the Lyda Hill Department of Bioinformatics at UTSW.

“Taken together, these two programs provide a more complete picture of how changes in DNA sequence, even in noncoding regions, can have dramatic effects on its spatial organization and function,” said Dr. Zhou, a member of the Harold C. Simmons Comprehensive Cancer Center, a Lupe Murchison Foundation Scholar in Medical Research, and a Cancer Prevention and Research Institute of Texas (CPRIT) Scholar.

Only about 1% of human DNA encodes instructions for making proteins. Research in recent decades has shown that much of the remaining noncoding genetic material holds regulatory elements – such as promoters, enhancers, silencers, and insulators – that control how the coding DNA is expressed. How sequence controls the functions of most of these regulatory elements is not well understood, Dr. Zhou explained.

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In a world first, scientists rewrite DNA to cure ‘genetic heart conditions’

By Mert Erdemir

An international team of scientists from the U.K., U.S., and Singapore is working together to develop an injectable cure for genetic heart conditions by rewriting DNA. The team named CureHeart has been awarded a £30 million grant from the British Heart Foundation (BHF).

The researchers will employ precision genetic techniques in the heart for the first time with the aim of silencing defective genes and develop and test the first treatment for genetic heart diseases. Animal tests had already proven before that the techniques work.

“This is a defining moment for cardiovascular medicine,” said Professor Sir Nilesh Samani, the BHF’s medical director. “Not only could CureHeart be the creators of the first cure for inherited heart muscle diseases by tackling killer genes that run through family trees, it could also usher in a new era of precision cardiology.”

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DNA Repair Kit Successfully Fixes Hereditary Disease in Cells

Image of patient derived podocyte kidney cells repaired with novel baculovirus-vectored approach pioneered by the Berger team. Podocin (coloured in green) is restored to the cell surface as in healthy podocytes. Credit: Dr Francesco Aulicino.Read time:  4 minutesDownload Article

Genetic mutations which cause a debilitating hereditary kidney disease affecting children and young adults have been fixed in patient-derived kidney cells using a potentially game-changing DNA repair-kit. The advance, developed by University of Bristol scientists, is published in Nucleic Acids Research.

In this new study, the international team describe how they created a DNA repair vehicle to genetically fix faulty podocin, a common genetic cause of inheritable Steroid Resistant Nephrotic Syndrome (SRNS).

Podocin is a protein normally located on the surface of specialised kidney cells and is essential for kidney function. Faulty podocin, however, remains stuck inside the cell and never makes it to the surface, terminally damaging the podocytes. Since the disease cannot be cured with medications, gene therapy which repairs the genetic mutations causing the faulty podocin offers hope for patients.

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Ultra-precise gene therapy technologies could edit or silence faulty genes causing fatal heart diseases

 By Emily Henderson, B.Sc.

An injectable cure for inherited heart muscle conditions that can kill young people in the prime of their lives could be available within a few years, after an international team of researchers were announced as the winners of the British Heart Foundation’s Big Beat Challenge.

The global award, at £30m, is one of the largest non-commercial grants ever given and presents a “once in a generation opportunity” to provide hope for families struck by these killer diseases.

The winning team, CureHeart, will seek to develop the first cures for inherited heart muscle diseases by pioneering revolutionary and ultra-precise gene therapy technologies that could edit or silence the faulty genes that cause these deadly conditions.

The team, made up of world-leading scientists from the UK, US and Singapore, was selected by an International Advisory Panel chaired by Professor Sir Patrick Vallance, Chief Scientific Advisor to the UK Government.

Inherited heart muscle diseases can cause the heart to stop suddenly or cause progressive heart failure in young people. Every week in the UK, 12 people under the age of 35 die of an undiagnosed heart condition1, very often caused by one of these inherited heart muscle diseases, also known as genetic cardiomyopathies. Around half of all heart transplants are needed because of cardiomyopathy and current treatments do not prevent the condition from progressing.

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A $100 genome? New DNA sequencers could be a ‘game changer’ for biology, medicine

The more than 3 billion letters in the human genome can now be sequenced for $100, several companies claim

“THIS IS THE YEAR OF THE BIG SHAKE-UP.”

For DNA sequencing, this “is the year of the big shake-up,” says Michael Snyder, a systems biologist at Stanford University. Sequencing is crucial to fields from basic biology to virology to human evolution, and its importance keeps growing. Clinicians are clamoring to harness it for early detection of cancer and other diseases, and biologists are finding ever more ways to use genomics to study single cells. But for years, most sequencing has relied on machines from a single company, Illumina.

Last week, however, a young company called Ultima Genomics said at a meeting in Orlando, Florida, that with new twists on existing technologies, it could provide human genomes for $100 a pop, one-fifth the going rate. Several other companies also promised faster, cheaper sequencing at the same meeting, Advances in Genome Biology and Technology. This year, key patents protecting Illumina’s sequencing technology will expire, paving the way for more competition, including from a Chinese company, MGI, which last week announced it would begin to sell its machines in the United States this summer. “We may be on the brink of the next revolution in sequencing,” says Beth Shapiro, an evolutionary biologist at the University of California, Santa Cruz (UCSC).

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A One-and-Done CRISPR Gene Therapy Will Aim to Prevent Heart Attacks

By Shelly Fan

In a few months, a daring clinical trial may fundamentally lower heart attack risk in the most vulnerable people. If all goes well, it will just take one shot.

It’s no ordinary shot. The trial, led by Verve Therapeutics, a biotechnology company based in Massachusetts, will be one of the first to test genetic base editors directly inside the human body. A variant of the gene editing tool CRISPR-Cas9, base editors soared to stardom when first introduced for their efficiency at replacing single genetic letters without breaking delicate DNA strands. Because it’s safer than the classic version of CRISPR, the new tool ignited hope that it could be used for treating genetic diseases.

Verve’s CEO, Dr. Sekar Kathiresan, took note. A cardiologist at Harvard University, Kathiresan wondered if base editing could help solve one of the main killers of our time: heart attacks. It seemed the perfect test case. We know one major cause of heart attacks—high cholesterol levels, particularly a version called LDL-C (Low-density lipoprotein cholesterol). We also know several major genes that control its level. And—most importantly—we know the DNA letter swap that can, in theory, drastically lower LDL-C and in turn throttle the risk of heart attacks.

There’s just one problem: we don’t know how base editors will behave inside a living human body.

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INSIDE PLANS FOR ‘OFF-WORLD HUMAN DNA SEED BANK’ ON MOON SO ALIEN CIVILIZATION COULD ‘RECREATE’ US

The SpaceX Crew-4 mission took some DNA to space on April 27

SPACEX just launched a lot of human DNA to the International Space Station. 

The Crew-4 mission blasted off on April 27 and part of the cargo was a biobank containing DNA from 500 different species.

One of those species was humans and there are now over 2,000 different DNA samples from lots of different people in space.

A company called LifeShip is behind the DNA collection.

It hopes to one day create an off-world genetic human seed bank on the Moon.

The idea is similar to the Global Seed Vault we have on Earth.

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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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