AI Enables Predictive Power for RNA-Targeting CRISPR Tools, Facilitating Precise Gene Control

According to a recent publication in Nature Biotechnology, researchers from New York University, Columbia Engineering, and the New York Genome Center have discovered that artificial intelligence (AI) can accurately predict the on- and off-target activity of CRISPR tools that target RNA instead of DNA. This groundbreaking study combines a deep learning model with CRISPR screens, enabling researchers to control the expression of human genes in various ways. This precise gene control could lead to the development of novel CRISPR-based therapies.

CRISPR technology has garnered significant attention due to its versatility in biomedical applications, ranging from treating genetic diseases like sickle cell anemia to enhancing the characteristics of crops. Traditionally, CRISPR targets DNA using the Cas9 enzyme. However, scientists have recently uncovered an alternative form of CRISPR that targets RNA using the Cas13 enzyme.

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New lipid nanoparticle CRISPR delivery system developed

A team of researchers from the University of California, Berkeley, and the University of Tokyo have developed a new delivery system for CRISPR gene editing technology using lipid nanoparticles. The technology allows for more efficient and targeted delivery of CRISPR components to specific cells in the body.

CRISPR technology has the potential to revolutionize medicine by allowing researchers to edit the genetic code of cells, potentially curing genetic diseases. However, one of the major challenges of CRISPR is delivering the necessary components, including the Cas9 enzyme and the guide RNA, to the target cells without causing adverse effects.

The researchers developed a lipid nanoparticle delivery system that can efficiently encapsulate and protect the CRISPR components, while also allowing for targeted delivery to specific cells. The system is based on a new type of lipid nanoparticle called a charged multilamellar vesicle (cMLV), which is made up of multiple layers of lipids with a positive charge on the outer layer.

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Researchers at the University of California, Santa Barbara, have developed a special drone that can collect environmental DNA (eDNA) from trees.


The drone, called the Spectral Phenotyping and Environmental Reconnaissance (SPEAR) system, is equipped with a hyperspectral camera and a custom-built eDNA sampler. The camera captures detailed images of the tree canopy, while the eDNA sampler collects genetic material from the leaves.

By analyzing the eDNA, researchers can identify the species of trees in the area, as well as the animals and insects that interact with them. This information can help scientists better understand the complex relationships between different species and the health of the ecosystem as a whole.

The SPEAR system has already been tested in a variety of environments, including tropical rainforests and oak woodlands. The drone’s ability to collect eDNA from trees offers a non-invasive and highly effective method for monitoring biodiversity and ecosystem health.

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Scientists reversed aging in mice. Is it possible in humans?

  • Aging is a natural part of life that changes the body in ways we sometimes might not like. 
  • Researchers from Harvard Medical School believe that epigenetic changes — and not just changes to the DNA — affect aging.
  • This view is supported by experiments where epigenetic changes caused mice to first age and the reversal of the induced changes caused reverse aging. 

Aging is a life process everyone goes through. As we age, the body changes in different ways — sometimes good and sometimes not as good as we might like. 

Scientists have looked for ways to slow down, stop, or reverse the aging process. While research and medical advances have helped increase life expectancy, aging continues. 

For many years, most researchers have believed changes to a body’s DNA — called mutations — are a leading cause of aging. 

Now a team led by researchers from Harvard Medical School finds support for an alternative hypothesis: it is the changes that affect the expression of the DNA — called epigenetics — that affect aging. Scientists demonstrated this via a mouse model where changes in epigenetic information caused mice to first age and then reverse aging. 

The study appears in the journal Cell

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New nanocapsules deliver therapy brain-wide, edit Alzheimer’s gene in mice

Researchers at UW–Madison have engineered silica nanocapsules to cross the blood-brain barrier in mice to deliver brain-wide gene editing therapy for Alzheimer’s disease. 

By Laura Red Eagle

Gene therapies have the potential to treat neurological disorders like Alzheimer’s and Parkinson’s diseases, but they face a common barrier — the blood-brain barrier. Now, researchers at the University of Wisconsin–Madison have developed a way to move therapies across the brain’s protective membrane to deliver brain-wide therapy with a range of biological medications and treatments.

“There is no cure yet for many devastating brain disorders,” says Shaoqin “Sarah” Gong, UW–Madison professor of ophthalmology and visual sciences and biomedical engineering and researcher at the Wisconsin Institute for Discovery. “Innovative brain-targeted delivery strategies may change that by enabling noninvasive, safe and efficient delivery of CRISPR genome editors that could, in turn, lead to genome-editing therapies for these diseases.”

CRISPR is a molecular toolkit for editing genes (for example, to correct mutations that may cause disease), but the toolkit is only useful if it can get through security to the job site. The blood-brain barrier is a membrane that selectively controls access to the brain, screening out toxins and pathogens that may be present in the bloodstream. Unfortunately, the barrier bars some beneficial treatments, like certain vaccines and gene therapy packages, from reaching their targets because in lumps them in with hostile invaders.

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New RNA Tool Can Illuminate Brain Circuits and Edit Specific Cells

Tagging and illuminating only the inhibitory “brake” cells (green) in human brain tissue is just one of many things the new tool from Duke University, CellREADR, can do.

Editing technology is precise and broadly applicable to all tissues and species.

Scientists at Duke University have developed an RNA-based editing tool that targets individual cells, rather than genes. It is capable of precisely targeting any type of cell and selectively adding any protein of interest.

Researchers said the tool could enable modifying very specific cells and cell functions to manage disease.

Using an RNA-based probe, a team led by neurobiologist Z. Josh Huang, Ph.D. and postdoctoral researcher Yongjun Qian, Ph.D. demonstrated they can introduce into cells fluorescent tags to label specific types of brain tissue; a light-sensitive on/off switch to silence or activate neurons of their choosing; and even a self-destruct enzyme to precisely expunge some cells but not others. The work will be published today (October 5, 2022) in the journal Nature.

Their selective cell monitoring and control system relies on the ADAR enzyme, which is found in every animal’s cells. While these are early days for CellREADR (Cell access through RNA sensing by Endogenous ADAR), the possible applications appear to be endless, Huang said, as is its potential to work across the animal kingdom.

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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


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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