In the summer of 2015, a 7-year-old named Hassan was admitted to the burn unit of the Ruhr University Children’s Hospital in Bochum, Germany, with red, oozing wounds from head to toe.
It wasn’t a fire that took his skin. It was a bacterial infection, resulting from an incurable genetic disorder. Called junctional epidermolysis bullosa, the condition deprives the skin of a protein needed to hold its layers together and leads to large, painful lesions. For kids, it’s often fatal. And indeed, Hassan’s doctors told his parents, Syrian refugees who had fled to Germany, the young boy was dying.
Since the first sequencing of the human genome more than 20 years ago, the study of human genomes has relied almost exclusively on a single reference genome to which others are compared to identify genetic variations. Scientists have long recognized that a single reference genome cannot represent human diversity and that using it introduces a pervasive bias into these studies. Now, they finally have a practical alternative.
In a paper published December 16 in Science, researchers at the UC Santa Cruz Genomics Institute have introduced a new tool, called Giraffe, that can efficiently map new genome sequences to a "pangenome" representing many diverse human genome sequences. They show that this approach allows a more comprehensive characterization of genetic variations and can improve the genomic analyses used by a wide range of researchers and clinicians.
"We've been working toward this for years, and now for the first time we have something practical that works fast and works better than the single reference genome," said corresponding author Benedict Paten, associate professor of biomolecular engineering at UC Santa Cruz and associate director of the Genomics Institute. "It's important for the future of biomedicine that genomics helps everyone equally, so we need tools that account for the diversity of human populations and are not biased."
A new ultra-rapid genome sequencing approach developed by Stanford Medicine scientists and their collaborators was used to diagnose rare genetic diseases in an average of eight hours—a feat that's nearly unheard of in standard clinical care.
"A few weeks is what most clinicians call 'rapid' when it comes to sequencing a patient's genome and returning results," said Euan Ashley, MB ChB, DPhil, professor of medicine, of genetics and of biomedical data science at Stanford.
Genome sequencing allows scientists to see a patient's complete DNA makeup, which contains information about everything from eye color to inherited diseases. Genome sequencing is vital for diagnosing patients with diseases rooted in their DNA: Once doctors know the specific genetic mutation, they can tailor treatments accordingly.
Now, a mega-sequencing approach devised by Ashley and his colleagues has redefined "rapid" for genetic diagnostics: Their fastest diagnosis was made in just over seven hours. Fast diagnoses mean patients may spend less time in critical care units, require fewer tests, recover more quickly and spend less on care. Notably, the faster sequencing does not sacrifice accuracy.
A paper describing the researchers' work will publish Jan.12 in The New England Journal of Medicine. Ashley, associate dean of the Stanford School of Medicine and the Roger and Joelle Burnell Professor in Genomics and Precision Health, is the senior author of the paper. Postdoctoral scholar John Gorzynski, DVM, Ph.D., is the lead author.
Nearly a decade ago, scientists discovered the power of CRISPR, a tool employed by bacteria to protect themselves against viral invaders. This system is now a fundamental research tool used for editing genomes. One of most popular CRISPR tool is CRISPR-Cas9, with which researchers can identify and then cut out or replace the targeted DNA within a cell.
"However, the ability of cas9 tools to engineer large-scale, gene-sized edits is really limited," said Yan Zhang, Ph.D., assistant professor in the Department of Biological Chemistry at the University of Michigan Medical School.
That's where another editing tool, CRISPR-Cas3, comes in.
In 2019, the Zhang lab was among the first wave of researchers to describe the new tool, which has the capability of processive DNA degradation and thereby making large scale genome deletions. The average human gene is 10 to 15 kilobases long, well within the ability of CRISPR-Cas3 to cut out.
CRISPR-Cas13 technique targets proteins causing ALS and Huntington's disease in the mouse nervous system https://medicalxpress.com/news/2022-01- ... ngton.html
by Liz Ahlberg Touchstone, University of Illinois at Urbana-Champaign
A single genetic mutation can have profound consequences, as demonstrated in neurodegenerative diseases such as amyotrophic lateral sclerosis or Huntington's disease. A new study by University of Illinois Urbana-Champaign researchers used a targeted CRISPR technique in the central nervous systems of mice to turn off production of mutant proteins that can cause ALS and Huntington's disease.
Rather than the popular DNA-editing CRISPR-Cas9 technique, the new approach uses CRISPR-Cas13, which can target mRNA—the messenger molecule that carries protein blueprints transcribed from DNA. The Illinois team developed Cas13 systems to target and cut RNAs that code for mutant proteins that trigger ALS and Huntington's disease, effectively silencing the mutant genes without disturbing the cell's DNA, said study leader Thomas Gaj, an Illinois professor of bioengineering. The team published its results in the journal Science Advances.
CRISPR genome editing has served as a powerful tool for deleting or altering DNA sequences and studying the resulting effect. Now, researchers at Gladstone Institutes and UC San Francisco (UCSF) have co-opted the CRISPR-Cas9 system to forcibly activate genes—rather than edit them—in human immune cells. The method, known as CRISPRa, let them discover genes that play a role in immune cell biology more thoroughly and rapidly than previously possible.
"This is an exciting breakthrough that will accelerate immunotherapy research," says Alex Marson, MD, Ph.D., director of the Gladstone-UCSF Institute of Genomic Immunology and senior author of the new study. "These CRISPRa experiments create a Rosetta Stone for understanding which genes are important for every function of immune cells. In turn, this will give us new insight into how to genetically alter immune cells so they can become treatments for cancer and autoimmune diseases."
The study, published in the journal Science, is the first to successfully use CRISPRa at a large scale in primary human cells, which are cells isolated directly from a person.
The scientists activated each gene in the genome in different cells, enabling them to test almost 20,000 genes in parallel. This allowed them to quickly learn the rules about which genes provide the most powerful levers to reprogram cell functions in ways that could eventually lead to more powerful immunotherapies.
Defective mitochondria—the 'batteries' that power the cells of our bodies—could in future be repaired using gene-editing techniques. Scientists at the University of Cambridge have shown that it is possible to modify the mitochondrial genome in live mice, paving the way for new treatments for incurable mitochondrial disorders.
Our cells contain mitochondria, which provide the energy for our cells to function. Each of these mitochondria is coded for by a tiny amount of mitochondrial DNA. Mitochondrial DNA makes up only 0.1% of the overall human genome and is passed down exclusively from mother to child.
Faults in our mitochondrial DNA can affect how well the mitochondria operate, leading to mitochondrial diseases, serious and often fatal conditions that affect around 1 in 5,000 people. The diseases are incurable and largely untreatable.
There are typically around 1,000 copies of mitochondrial DNA in each cell, and the percentage of these that are damaged, or mutated, will determine whether a person will suffer from mitochondrial disease or not. Usually, more than 60% of the mitochondria in a cell need to be faulty for the disease to emerge, and the more defective mitochondria a person has, the more severe their disease will be. If the percentage of defective DNA could be reduced, the disease could potentially be treated.
Since the discovery of CRISPR/Cas9, also known as molecular scissors, scientists around the world have been working to improve the revolutionary technique for altering DNA that earned Emmanuelle Charpentier and Jennifer Doudna the Nobel Prize in 2020. The method enables deep exploration of the human genome and shows enormous potential for curing genetic diseases. While the precise alterations made by CRISPR/Cas9 were initially less predictable, scientists around the world are now working on further developments that enable precise changes to be made within DNA. A recent study by the group of Joanna Loizou, Group Leader at the Center for Cancer Research at MedUni Vienna and CeMM Adjunct Principal Investigator, was devoted to understanding how prime editing, a technique that promises greater targeting accuracy and efficiency in introducing DNA changes, can be made more efficient and precise.
Prime editing is a powerful genome engineering tool that allows for replacement, insertions, and deletion of DNA into any given genomic locus. However, to date, the efficiency of prime editing has been highly variable and depends not only on the targeted genomic region but also on the genetic background of the edited cell. Leading authors Joana Ferreira da Silva, CeMM Ph.D. student, and Gonçalo Oliveira from the Center for Cancer Research of the MedUni Vienna, devoted their study to the question of which factors influence the success of prime editing, taking a close look at DNA repair processes. Since genome editing relies on the intrinsic DNA repair machinery within a cell, it is imperative to know which DNA repair pathways are engaged and how this impacts the outcome of editing. Yet the underlying DNA repair machinery involved in prime editing is largely unknown. The study authors explain that "depending on the type of DNA damage, a cell has different cellular repair mechanisms. To find out which of these are active in prime editing, we performed a targeted genetic screening for DNA repair factors covering all known repair pathways."
Abstract
DNA nanostructures are a promising tool to deliver molecular payloads to cells. DNA origami structures, where long single-stranded DNA is folded into a compact nanostructure, present an attractive approach to package genes; however, effective delivery of genetic material into cell nuclei has remained a critical challenge. Here, we describe the use of DNA nanostructures encoding an intact human gene and a fluorescent protein encoding gene as compact templates for gene integration by CRISPR-mediated homology-directed repair (HDR). Our design includes CRISPR-Cas9 ribonucleoprotein binding sites on DNA nanostructures to increase shuttling into the nucleus. We demonstrate efficient shuttling and genomic integration of DNA nanostructures using transfection and electroporation. These nanostructured templates display lower toxicity and higher insertion efficiency compared to unstructured double-stranded DNA templates in human primary cells. Furthermore, our study validates virus-like particles as an efficient method of DNA nanostructure delivery, opening the possibility of delivering nanostructures in vivo to specific cell types. Together, these results provide new approaches to gene delivery with DNA nanostructures and establish their use as HDR templates, exploiting both their design features and their ability to encode genetic information. This work also opens a door to translate other DNA nanodevice functions, such as biosensing, into cell nuclei.
One of the grand challenges with using CRISPR-based gene editing on humans is that the molecular machinery sometimes makes changes to the wrong section of a host's genome, creating the possibility that an attempt to repair a genetic mutation in one spot in the genome could accidentally create a dangerous new mutation in another.
But now, scientists at The University of Texas at Austin have redesigned a key component of a widely used CRISPR-based gene-editing tool, called Cas9, to be thousands of times less likely to target the wrong stretch of DNA while remaining just as efficient as the original version, making it potentially much safer. The work is described in a paper published today in the journal Nature.
"This really could be a game changer in terms of a wider application of the CRISPR Cas systems in gene editing," said Kenneth Johnson, a professor of molecular biosciences and co-senior author of the study with David Taylor, an assistant professor of molecular biosciences. The paper's co-first authors are postdoctoral fellows Jack Bravo and Mu-Sen Liu.
Other labs have redesigned Cas9 to reduce off-target interactions, but so far, all these versions improve accuracy by sacrificing speed. SuperFi-Cas9, as this new version has been dubbed, is 4,000 times less likely to cut off-target sites but just as fast as naturally occurring Cas9. Bravo says you can think of the different lab-generated versions of Cas9 as different models of self-driving cars. Most models are really safe, but they have a top speed of 10 miles per hour.
(EurekAlert) By combining CRISPR technology with a protein designed with artificial intelligence, it is possible to awaken individual dormant genes by disabling the chemical “off switches” that silence them. Researchers from the University of Washington School of Medicine in Seattle describe this finding in the journal Cell Reports.
The approach will allow researchers to understand the role individual genes play in normal cell growth and development, in aging, and in such diseases as cancer, said Shiri Levy, a postdoctoral fellow in UW Institute for Stem Cell and Regenerative Medicine (ISCRM) and the lead author of the paper.
“The beauty of this approach is we can safely upregulate specific genes to affect cell activity without permanently changing the genome and cause unintended mistakes,” Levy said.
Researchers from the TU Delft have come up with a physical-based model that establishes a quantitative framework on how gene-editing with CRISPR-Cas9 works, and allows them to predict where, with what probability, and why targeting errors (off-targets) occur. This research, which has been published in Nature Communications, gives us a first detailed physical understanding of the mechanism behind the most important gene editing platform of today.
The discovery of the CRISPR-Cas9 protein has greatly simplified gene editing, and raised hopes to find a cure to many hereditary diseases. However, routine and safe use of this technique in human therapeutics requires extreme precision and predictability of any off-target effects. A research team lead by Martin Depken at TU Delft's department of Bionanoscience has now demonstrated a new, physical-based model that greatly improves on existing models: not only does the model predict where the DNA is likely to be cut, but also with what probability this will happen.
Physics-based approach to understand Cas9 gene-editing
A great limitation of current bioinformatics models for gene editing lies in the fact that they are binary in nature: they classify targets on the genome as either likely or unlikely to be cut. These models focus only on very high-probability targeting errors (off-targets), and will miss the many lower probability off-targets that together could amount to the majority of editing errors in the genome. Now, the new physical model which the researchers created takes into account both high-probability and low-probability off-targets; it can be used to physically characterize any Cas9 variant and predict the probability that any site will be cleaved.
Martin Depken explains his lab's new physics-based approach: "In gene editing, you want to maximize the probability of cutting at the intended site, while minimizing the amount of cutting in the rest of the genome. It is therefore crucial to understand cutting in terms of probabilities. Drawing from experiments in single-molecule physics and structural data, we created a model that can do this. We changed the way in which to describe the gene editing from a binary choice to a complete probabilistic picture."
(IFL Science) The first fully complete human genome with no gaps is now available to view for scientists and the public, marking a huge moment for human genetics. Announced in a preprint in June 2021, six papers have now been published in the journal Science. They describe the painstaking work that goes into sequencing an over 6 billion base pair genome, with 200 million added in this new research. The new genome now adds 99 genes likely to code for proteins and 2,000 candidate genes that were previously unknown.
Many will be asking: "wait, didn’t we already sequence the human genome?" In part, yes – in 2000, the Human Genome Sequencing Consortium published their first drafts of the human genome, results that subsequently paved the way for almost every facet of human genetics available today.
The most recent draft of the human genome has been used as a reference since 2013. But weighed down by impractical sequencing techniques, these drafts left out the most complex regions of our DNA, which make up around 8 percent of the total genome. This is because these sequences are highly repetitive and contain many duplicated regions – attempting to put them together in the right places is like trying to complete a jigsaw puzzle where all the pieces are the same shape and have no image on the front. Long gaps and underrepresentation of large, repeating sequences made it so that this genetic material has been excluded for the past 20 years. Scientists had to come up with more accurate methods of sequencing to illuminate the darkest corners of the genome.
“These parts of the human genome that we haven’t been able to study for 20-plus years are important to our understanding of how the genome works, genetic diseases, and human diversity and evolution,” said Karen Miga, assistant professor of biomolecular engineering at UC Santa Cruz, in a statement.
Much like the Human Genome Sequencing Consortium, the new reference genome (called T2T-CHM13) was produced by the Telomere-2-Telomere Consortium, a group of researchers dedicated to finally mapping each chromosome from one telomere to the other. T2T-CHM13 will now be available on UCSC Genome Browser for everyone to enjoy, complimenting the standard human reference genome, GRCh38.
WEHI researchers have revealed how an "accordion effect" is critical to switching off genes, in a study that transforms the fundamentals of what we know about gene silencing.
The finding expands our understanding of how we switch genes on and off to make the different cell types in our bodies, as we develop in the womb.
It also offers a new way to potentially harness gene silencing in the future, to treat or reverse the progression of a broad range of diseases including cancer, congenital and infectious diseases.
Gene silencing is regulated by how tightly DNA is packed into a cell. The findings from a team led by Dr. Andrew Keniry and Professor Marnie Blewitt reveal a new accordion-like trigger that is crucial to the process.
The research is published in Nature Communications.
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.
A critical challenge in gene therapy remains the safe and effective delivery of genetic materials, and most methods in use today are costly, inefficient, imprecise or potentially toxic. The KAUST-devised delivery system could offer an improved means of regulating gene expression and function in people's cells as a way of treating cancer, hemophilia and many more genetic disorders.
Given enough time and energy, the body will heal, but when doctors or engineers intervene, the processes do not always proceed as planned because chemicals that control and facilitate the healing process are missing. Now, an international team of engineers is bioprinting bone along with two growth factor encoding genes that help incorporate the cells and heal defects in the skulls of rats.
"Growth factors are essential for cell growth," said Ibrahim T. Ozbolat, associate professor of engineering science and mechanics. "We use two different genes encoding two different growth factors. These growth factors help stem cells to migrate into the defect area and then help the progenitor cells to convert into bone."
The researchers used gene encoding PDGF-B, platelet derived-growth factor, which encourages cells to multiply and to migrate, and gene encoding BMP-2, bone morphogenetic protein, which improves bone regeneration. They delivered both genes using bioprinting.
"We used a controlled co-delivery release of plasmids from a gene-activated matrix to promote bone repair," the researchers stated in the journal Biomaterials.
Researchers from the Center for Genome Engineering within the Institute for Basic Science developed a new gene-editing platform called transcription activator-like effector-linked deaminases, or TALED. TALEDs are base editors capable of performing A-to-G base conversion in mitochondria. This discovery was a culmination of a decades-long journey to cure human genetic diseases, and TALED can be considered to be the final missing piece of the puzzle in gene-editing technology.
From the identification of the first restriction enzyme in 1968, the invention of polymerase chain reaction (PCR) in 1985, and the demonstration of CRISPR-mediated genome editing in 2013, each new breakthrough discovery in biotechnology further improved our ability to manipulate DNA, the blueprint of life. In particular, the recent development of the CRISPR-Cas system, or "genetic scissors," has allowed for comprehensive genome editing of living cells. This opened new possibilities for treating previously incurable genetic diseases by editing the mutations out of our genome.
(EurekAlert) Scientists at UC Riverside have a shot at eradicating a deadly threat to vineyards posed by the glassy-winged sharpshooter, just as its resistance to insecticide has been growing.
When the half-inch-long flying insect feeds on grapevines, it transmits bacteria that causes Pierce’s Disease. Once infected, a vine is likely to die within three years — a growing problem for California’s $58 billion wine industry. Currently, it can only be controlled with quarantines and increasingly less effective chemical sprays.
New gene-editing technology represents hope for controlling the sharpshooter. Scientists at UC Riverside demonstrated that this technology can make permanent physical changes in the insect. They also showed these changes were passed down to three or more generations of insects.
“Our team established, for the first time, genetic approaches to controlling glassy-winged sharpshooters,” said Peter Atkinson, entomologist and paper co-author.
The most common cause of spontaneous abortions is chromosome defects, but they can be difficult to detect. Researchers from the University of Copenhagen have developed a new method that can make us wiser about how chromosome defects and disease-associated chromosome changes look and how to aid diagnosis.
In Denmark, more and more people are experiencing problems with fertility. The most common cause of spontaneous abortion is chromosome defects. In more than half of the miscarriages that occur during the first 12 weeks, it is because the fetus has a chromosome defect.
Often doctors do not know which chromosome defect is involved. Therefore, it is also difficult to know what the parents can do to complete the pregnancy successfully. However, new research from the University of Copenhagen may help to clarify this.
A newly developed method can characterize chromosomes with an unprecedented level of detail and may help uncover new chromosome errors, which cannot be diagnosed with current methods.
Humble potatoes are a rich source not only of dietary carbohydrates for humans, but also of starches for numerous industrial applications. Texas A&M AgriLife scientists are learning how to alter the ratio of potatoes' two starch molecules—amylose and amylopectin—to increase both culinary and industrial applications.
For example, waxy potatoes, which are high in amylopectin content, have applications in the production of bioplastics, food additives, adhesives and alcohol.
Two articles recently published in the International Journal of Molecular Sciences and the Plant Cell, Tissue and Organ Culture journals outline how CRISPR technology can advance the uses of the world's largest vegetable crop.
Both papers include the work done by Stephany Toinga, Ph.D., who was a graduate student in the lab of Keerti Rathore, Ph.D., AgriLife Research plant biotechnologist in the Texas A&M Institute for Plant Genomics and Biotechnology and Department of Soil and Crop Sciences. Also co-authoring both papers was Isabel Vales, Ph.D., an AgriLife Research potato breeder in the Texas A&M Department of Horticultural Sciences. Toinga is now a Texas A&M AgriLife Research postdoctoral associate with Vales.
"The information and knowledge we gained from these two studies will help us introduce other desirable traits in this very important crop," Rathore said.
