The 1997 film Gattaca promised a future where humans would be free of disease and babies born on demand with the latest upgrades, including enhanced speed, intelligence, and beauty. Much like a new Tesla Roadster. However, despite the technological predictions offered by Hollywood moviemakers, were still living in a time when synthetic biology is working hard to make a dent in the world. No designer babies in sight. And stem cell technology promised so many radical breakthroughs back in the late 1990s, including growing organs for transplants and regenerating whole body parts, but the challenge of growing whole organs has been shown to be more complex than previously believed, including technologies like 3D bioprinting and xenotransplantation.

Despite the challenges and setbacks, investors believe were living in a different time, with more money pouring into the space over the last few years:

Indeed, the science and technology behind manipulating biological matter are still promising when it comes to health and medicine, especially with the rise of CRISPR gene editing. The idea that we could potentially switch on or off genes that cause disease using a cocktail of enzymes is just fantastical. While inserting CRISPR enzymes into a live human being is a bit challenging, there are regions of the body that are easily accessible, such as the eye. In a landmark clinical trial approved by the FDA and led by Editas Medicine (EDIT) and Allergan, now owned by AbbVie (ABBV), a CRISPR-Cas9 gene therapy was administered directly to patients to remove rare mutations that can cause childhood blindness.

McKinsey is calling this emerging technological renaissance the next Bio Revolution, with advances in biological sciences being accelerated by automation and artificial intelligence. The speed at which scientists and researchers were able to sequence the genome of the Rona virus is a testament to the power of these converging technologies. McKinsey predicts that synthetic biology could have a direct economic impact of $4 trillion per year, nearly half of which will be in the domain of human health.

Lets take a look through five companies that are harnessingthe revolutionary power of synthetic biology to design new therapies and treathuman diseases.

Founded in 2017 and headquartered in Alameda, California, Scribe Therapeutics is a biotechnology startup that is producing therapeutics using custom-engineered CRISPR enzyme technology. The company has raised a whopping $120 million from the likes of Andreessen Horowitz to build out a suite of CRISPR technologies designed to treat genetic diseases. Scribe Therapeutics was co-founded by Dr. Jennifer Doudna, the UC Berkeley biochemist who discovered and developed CRISPR gene-editing technology and won the Nobel Prize in Chemistry in 2020 for her pioneering work.

The team at Scribe Therapeutics has designed its XEditing (XE) technology by evolving the native CRISPR gene-editing enzymes available to us to redesign and engineer them to suit different needs. More specifically, they want to be able to modify or silence the genes of live humans to treat genetic diseases such as Huntingtons, Parkinsons, Sickle Cell Anemia, and Amyotrophic Lateral Sclerosis (ALS). Anything your parents unwittingly handed down to you, Scribe Therapeutics is looking to treat it. The research team tests thousands of redesigned enzymes and selects those with greater editing ability, specificity, and stability compared to current enzymes. Scribe Therapeutics is starting with a pipeline of therapeutics to treat neurodegenerative diseases and has its sights set on other, less common genetic conditions down the road.

Canadian biotechnology startup Notch Therapeutics was founded in 2018 and has raised $86 million to develop immune cell therapies against pre-cancer cells. The companys cell therapies are based on induced pluripotent stem cells (iPSC), which are pre-differentiated cells with the limited capacity to transform into different mature cell lines. Based on its Engineered Thymic Niche (ETN) platform, the company is developing universally compatible stem cell-derived immune cell therapies.

Normally, human immune cells only recognize othercells found in the same individual and will target cells from other individuals,which appear foreign to the immune system. Thats why donor organs can sometimesbe rejected by the recipients body the immune system sees the organ as a foreignobject. Notch Therapeutics is designing a system where the immune cellsproduced from the stem cells will be universally recognizable by allindividuals, bypassing the need to create immune cells from pluripotent stemcells derived from each recipient. These manufactured immune cells, whichinclude T cells or natural killer cells, can be programmed to target cancercells and eliminate them from the patient.

Founded in 2016, Massachusetts-based bit.bio is a synthetic biology startup thats working on merging the world of coding with biology. The company has secured $42 million after a Series A round that was completed in June 2020. A spinout of Cambridge University, bit.bio is looking to commercialize its proprietary platform, opti-ox, which can reprogram human stem cells to do its bidding cure diseases. Touted as the Cell Coding Company, bit.bio was founded by Dr. Mark Kotter, a neurosurgeon at the University of Cambridge who studied regenerative medicine and stem cell technology.

While the ability to program mammalian stem cells has been around since 1981, the company claims it can consistently reprogram human adult cells into pluripotent stem cells, and then transform them into other mature human cells within days. Currently, stem cell technology produces a statistical mixed bag of mature, differentiated cells, some of which can have potential side effects. opti-ox uses a precise combination of transcription factors to ensure stem cells mature into cardiac, muscle, liver, kidney, or lung cells with high efficiency. The holy grail for the company is to be able to produce every cell in the human body for any cell therapy safely, on-demand, and with purities approaching 100%. And well be here, waiting for that stem cell therapy for erectile dysfunction promised by the medical community.

Founded in 2020, Delonix Bioworks is a Shanghai-based synthetic biology company designing therapeutic solutions against infectious diseases. The startup received $14 million from a Seed round just back in March. The Delonix Bioworks team is focusing its initial efforts on anti-microbial resistant (AMR) infections. The emergence of resistance in some bacteria species against common antimicrobial compounds, so has led to an increasing number of infections that are difficult to treat with conventional strategies. These superbug strains are mostly spread in hospital or clinical settings due to the overuse of antibiotics.

The company is engineering attenuated, live bacteria thatcan act as vaccines against these types of infections. By introducing reprogrammed,but weakened, bacteria to express specific antigens on the surface of theirmembrane that match those of the strains that cause AMR infections into anindividual, the individuals immune system can recognize those antigens andrespond to future infections with greater speed. Its no different from how antiviralvaccines are designed, except most vaccines introduce an attenuated or inactivatedvirus to activate the immune system instead. And for those of you who skipped highschool biology, no, this is not a mind-control scheme orchestrated by biotech companies.

Founded in 2018, Octarine Bio is a Danish synthetic biology company thats building out a pipeline for high-potency cannabinoids and psilocybin derivatives for the pharmaceutical industry. Octarine Bio has brought in $3 million after a Seed round that was also completed in March. Medical studies on psychotropic compounds have been shown to help reduce anxiety, depression, and pain, and may have the potential to serve as novel psychiatric medications. A few companies have recently emerged to commercialize existing psychedelics. Octarine Bio believes it can do better by harnessing the power of synthetic biology to engineer microorganisms to produce these psychotropic compounds with better pharmacokinetic and therapeutic effects.

Normally, natural products are produced by plant and fungal species as an ill-defined mixture. The psychoactive properties of these compounds primarily stem from only a handful of compounds because their natural concentration is much higher than other derivatives in the organic material. For example, tetrahydrocannabinol (THC) is the main psychoactive agent in marijuana while psilocybin is the one found in mushrooms from the Psilocybe and other psilocybin-producing genera. However, these are just a few out of hundreds of potential psychoactive derivatives produced by these species.

Molecular derivatives may be produced at too low of concentration to test and analyze, or the plant or mushroom may have a deactivated metabolic pathway that could lead to a superior compound. By tweaking the molecular structure of the product compounds using both synthetic biology and traditional organic chemistry, the team at Octarine Bio is creating a platform to discover new potential therapeutics that may not have been available before. Magic mushrooms are about to get an upgrade for an extra potent trip.

Much like what was said about software by Marc Andreessen back in 2011, synthetic biology is starting to eat the world. While were a long way away from a dystopian future where babies are engineered with supernatural talents, were already seeing the potential side-effects of using CRISPR on the Chinese twin girls originally to immunize them from HIV, including enhanced cognition and memory. The cure for stupid is possibly lurking in the vaults of this pioneering technology. For now, well wait and see how synthetic biology and CRISPR gene editing shape up as potential therapeutics for real diseases.

Tech investing is extremely risky. Minimize your risk with The Nanalyze Disruptive Tech Portfolio Report to find out which tech stocks you should avoid. Become a Nanalyze Premium member and find out today!

Continued here:
5 Novel Therapies Using Synthetic Biology - Nanalyze

Synthego, the genome engineering company, today announced the launch of Eclipse, a new high-throughput cell engineering platform designed to accelerate drug discovery and validation by providing highly predictable CRISPR-engineered cells at scale through the integration of engineering, bioinformatics, and proprietary science. The launch of this unique CRISPR-based platform is driving the companys growing impact in biopharma R&D, reinforcing Synthegos position as the genome engineering leader.

CRISPR-engineered cells have a wide range of applications in research and development across disease areas, including in neuroscience and oncology. Synthego created the Eclipse Platform to enhance disease modeling, drug target identification and validation, and accelerate cell therapy manufacturing.

"By industrializing cell engineering, Synthegos Eclipse Platform will enable economies of scale, turning a historically complex process into one that is flexible, reliable, and affordable, said Bill Skarnes, Ph.D., professor and director of Cellular Engineering at The Jackson Laboratory and Synthego advisory board member. Offering CRISPR edits at scale, similar to what Synthego did with sgRNA reagents, puts researchers on the cusp of being able to study thousands of genes, and examine hundreds of variants of those genes. This will allow scientists to more faithfully model the complexity of a human disease, which could lead to the development of therapeutic drugs or next-generation gene therapies for many serious diseases.

To ensure the success of any type of edit, Eclipse uses machine learning to apply experience from several hundred thousand genome edits across hundreds of cell types. With this machine learning, combined with automation, the new platform can reduce costs and increase the scalability of engineered cell production. The Eclipse Platform is modular in design, allowing for fast deployment of upgrades or add-ons. It is engineered to use a cell-type agnostic process and immediately benefit researchers working with induced pluripotent stem (iPS) cells and immortalized cell lines.

We are living in a new era of life sciences innovation one that has added to DNA sequencing and being able to read out of biology, now being able to write into and engineer biology. We created our Eclipse Platform at the convergence of science and technology to make genome editing more precise, scalable, and accessible, said Paul Dabrowski, CEO and co-founder of Synthego. We are excited to expand our impact on advancing the life sciences innovation with the launch of this unique CRISPR-based platform.

Go here to read the rest:
Synthego Launches Eclipse Platform to Accelerate Research and Development of Next-generation Medicines - The Scientist

When it comes to Alzheimers versus science, science is on the losing side.

Alzheimers is cruel in the most insidious way. The disorder creeps up in some aging brains, gradually eating away at their ability to think and reason, whittling down their grasp on memories and reality. As the worlds population ages, Alzheimers is rearing its ugly head at a shocking rate. And despite decades of research, we have no treatmentnot to mention a cure.

Too much of a downer? The National Institutes of Health (NIH) agrees. In one of the most ambitious projects in biology, the NIH is corralling Alzheimers and stem cell researchers to come together in the largest genome editing project ever conceived.

The idea is simple: decades of research have found certain genes that seem to increase the chance of Alzheimers and other dementias. The numbers range over hundreds. Figuring out how each connects or influences anotherif at alltakes years of research in individual labs. What if scientists unite, tap into a shared resource, and collectively solve the case of why Alzheimers occurs in the first place?

The initiatives secret weapon is induced pluripotent stem cells, or iPSCs. Similar to most stem cells, they have the ability to transform into anythinga cellular Genie, if you will. iPSCs are reborn from regular adult cells, such as skin cells. When transformed into a brain cell, however, they carry the original genes of their donor, meaning that they harbor the original persons genetic legacyfor example, his or her chance of developing Alzheimers in the first place. What if we introduce Alzheimers-related genes into these reborn stem cells, and watch how they behave?

By studying these iPSCs, we might be able to follow clues that lead to the genetic causes of Alzheimers and other dementiaspaving the road for gene therapies to nip them in the bud.

The iPSC Neurodegenerative Disease Initiative (iNDI) is set to do just that. The project aims to stimulate, accelerate, and support research that will lead to the development of improved treatments and preventions for these diseases, the NIH said. All resulting datasets will be openly shared online, for anyone to mine and interpret.

In plain language? Lets throw all of our new biotech superstarswith CRISPR at the forefrontinto a concerted effort against Alzheimers, to finally gain the upper hand. Its an Avengers, assemble moment towards one of our toughest foesone that seeks to destroy our own minds from within.

Alzheimers disease was first recognized in the early 1900s. Ever since, scientists have strived to find the cause that makes a brain waste away.

The most prominent idea today is the amyloid hypothesis. Imagine a horror movie inside a haunted house with ghosts that gradually intensify in their haunting. Thats the amyloid horrora protein that gradually but silently builds up inside a neuron, the house, eventually stripping it of its normal function and leading to the death of anything inside. Subsequent studies also found other toxic proteins that hang around outside the neuron house that gradually poison the molecular tenants within.

For decades scientists have thought that the best approach to beat these ghosts was an exorcismthat is, to get rid of these toxic proteins. Yet in trial after trial, they failed. The failure rate for Alzheimers treatmentso far, 100 percenthas led some to call treatment efforts a graveyard of dreams.

Its pretty obvious we need new ideas.

A few years ago, two hotshots strolled into town. One is CRISPR, the wunderkind genetic sharpshooter that can snip way, insert, or swap out a gene or two (or more). The other is iPSCs, induced pluripotent stem cells, which are reborn from adult cells through a chemical bath.

The two together can emulate Dementia 2.0 in a dish.

For example, using CRISPR, scientists can easily insert genes related to Alzheimers, or its protection, into an iPSCeither that from a healthy donor, or someone with a high risk of dementia, and observe what happens. A brain cell is like a humming metropolitan area, with proteins and other molecules whizzing around. Adding in a dose of pro-Alzheimers genes, for example, could block up traffic with gunk, leading scientists to figure out how those genes fit into the larger Alzheimers picture. For the movie buffs out there, its like adding into a cell a gene for Godzilla and another for King Kong. You know both could mess things up, but only by watching what happens in a cell can you know for sure.

Individual labs have tried the approach since iPSCs were invented, but theres a problem. Because iPSCs inherit the genetic baseline of a person, it makes it really difficult for scientists in different labs to evaluate whether a gene is causing Alzheimers, or if it was just a fluke because of the donors particular genetic makeup.

The new iNDI plan looks to standardize everything. Using CRISPR, theyll add in more than 100 genes linked to Alzheimers and related dementias into iPSCs from a wide variety of ethnically diverse healthy donors. The result is a huge genome engineering project, leading to an entire library of cloned cells that carry mutations that could lead to Alzheimers.

In other words, rather than studying cells from people with Alzheimers, lets try to give normal, healthy brain cells Alzheimers by injecting them with genes that could contribute to the disorder. If you view genes as software code, then its possible to insert code that potentially drives Alzheimers into those cells through gene editing. Execute the program, and youll be able to observe how the neurons behave.

The project comes in two phases. The first focuses on mass-engineering cells edited with CRISPR. The second is thoroughly analyzing these resulting cells: for example, their genetics, how their genes activate, what sorts of proteins they carry, how those proteins interact, and so on.

By engineering disease-causing mutations in a set of well-characterized, genetically diverse iPSCs, the project is designed to ensure reproducibility of data across laboratories and to explore the effect of natural variation in dementia, said Dr. Bill Skarnes, director of cellular engineering at the Jackson Laboratory, and a leader of the project.

iNDI is the kind of initiative thats only possible with our recent biotech boost. Engineering hundreds of cells related to Alzheimersand to share with scientists globallywas a pipe dream just two decades ago.

To be clear, the project doesnt just generate individual cells. It uses CRISPR to make cell lines, or entire lineages of cells with the Alzheimers gene that can pass on to the next generation. And thats their power: they can be shared with labs around the world, to further hone in on genes that could make the largest impact on the disorder. Phase two of iNDI is even more powerful, in that it digs into the inner workings of these cells to generate a cheat codea sheet of how their genes and proteins behave.

Together, the project does the hard work of building a universe of Alzheimers-related cells, each outfitted with a gene that could make an impact on dementia. These types of integrative analyses are likely to lead to interesting and actionable discoveries that no one approach would be able to learn in isolation, the authors wrote. It provides the best chance at truly understanding Alzheimers and related diseases, and promising treatment possibilities.

Image Credit: Gerd Altmann from Pixabay

Continued here:
A Massive New Gene Editing Project Is Out to Crush Alzheimer's - Singularity Hub

Novartis and the Bill and Melinda Gates Foundation are joining forces to discover and develop a gene therapy to cure sickle cell disease with a one-step, one-time treatment that is affordable and simple enough to treat patients anywhere in the world, especially in sub-Saharan Africa where resources may be scarce but disease prevalence is high.

The three-year collaboration, announced Wednesday, has initial funding of $7.28 million.

Current gene therapy approaches being developed for sickle cell disease are complex, enormously expensive, and bespoke, crafting treatments for individual patients one at a time. The collaboration aims to instead create an off-the-shelf treatment that bypasses many of the steps of current approaches, in which cells are removed and processed outside the body before being returned to patients.

advertisement

Sickle cells cause is understood. The people it affects are known. But its cure has been elusive, Jay Bradner, president of the Novartis Institutes for BioMedical Research, told STAT.

We understand perfectly the disease pathway and the patient, but we dont know what it would take to have a single-administration, in vivo gene therapy for sickle cell disease that you could deploy in a low-resource setting with the requisite safety and data to support its use, he said. Im a hematologist and can assure you that in my experience in the clinic, it was extremely frustrating to understand a disease so perfectly but have so little to offer.

advertisement

Sickle cell disease is a life-threatening inherited blood disorder that affects millions around the world, with about 80% of affected people in sub-Saharan Africa and more than 100,000 in the U.S. The mutation that causes the disease emerged in Africa, where it protects against malaria. While most patients with sickle cell share African ancestry, those with ancestry from South America, Central America, and India, as well as Italy and Turkey, can also have the hereditary disease.

The genetic mutation does its damage by changing the structure of hemoglobin, hampering the ability of red blood cells to carry oxygen and damaging blood vessels when the misshapen cells get stuck and block blood flow. Patients frequently suffer painful crises that can be fatal if not promptly treated with fluids, medication, and oxygen. Longer term, organs starved of oxygen eventually give out. In the U.S., that pain and suffering is amplified when systemic and individual instances of racism deny Black people the care they need.

Delivering gene therapy for other diseases has been costly and difficult even in the best financed, most sophisticated medical settings. Challenges include removing patients cells so they can be altered in a lab, manufacturing the new cells in high volume, reinfusing them, and managing sometimes severe responses to the corrected cells. Patients also are given chemotherapy to clear space in their bone marrow for the new cells.

Ideally, many of those steps could be skipped if there were an off-the-shelf gene therapy. That means, among other challenges, inventing a way to eliminate the step where each patients cells are manipulated outside the body and given back the in vivo part of the plan to correct the genetic mutation.

Thats not the only obstacle. For a sickle cell therapy to be successful, Bradner said, it must be delivered only to its targets, which are blood stem cells. The genetic material carrying corrected DNA must be safely transferred so it does not become randomly inserted into the genome and create the risk of cancer, a possibility that halted a Bluebird Bio clinical trial on Tuesday. The payload itself mustnt cause such problems as the cytokine storm of immune overreaction. And the intended response has to be both durable and corrective.

In a way, the gene delivery is the easy part because we know that expressing a normal hemoglobin, correcting the mutated hemoglobin, or reengineering the switches that once turned off normal fetal hemoglobin to turn it back on, all can work, Bradner said. The payload is less a concern to me than the safe, specific, and durable delivery of that payload.

For each of these four challenges delivery, gene transfer, tolerability, durability there could be a bespoke technical solution, Bradner said. The goal is to create an ensemble form of gene therapy.

Novartis has an existing sickle-cell project using CRISPR with the genome-editing company Intellia, now in early human trials, whose lessons may inform this new project. CRISPR may not be the method used; all choices are still on the table, Bradner said.

Vertex Pharmaceuticals has seen encouraging early signs with its candidate therapy developed with CRISPR Therapeutics. Other companies, including Beam Therapeutics, have also embarked on gene therapy development.

The Novartis-Gates collaboration is different in its ambition to create a cure that does not rely on an expensive, complicated framework. Novartis has worked with the Gates Foundation on making malaria treatment accessible in Africa. And in October 2019, the Gates Foundation and the National Institutes of Health said together they would invest at least $200 million over the next four years to develop gene-based cures for sickle cell disease and HIV that would be affordable and available in the resource-poor countries hit hardest by the two diseases, particularly in Africa.

Gene therapies might help end the threat of diseases like sickle cell, but only if we can make them far more affordable and practical for low-resource settings, Trevor Mundel, president of global health at the Gates Foundation, said in a statement about the Novartis collaboration. Its about treating the needs of people in lower-income countries as a driver of scientific and medical progress, not an afterthought.

Asked which is the harder problem to solve: one-time, in vivo gene therapy, or making it accessible around the world, David Williams, chief of hematology/oncology at Boston Childrens Hospital, said: Both are going to be difficult to solve. The first will likely occur before the therapy is practically accessible to the large number of patients suffering the disease around the world.

Williams is also working with the Gates Foundation, as well as the Koch Institute for Integrative Cancer Research at MIT, Dana-Farber Cancer Institute, and Massachusetts General Hospital, on another approach in which a single injection of a reagent changes the DNA of blood stem cells. But there are obstacles to overcome there, too, that may be solved by advances in both the technology to modify genes and the biological understanding of blood cells.

Bradner expects further funding to come to reach patients around the world, once the science progresses more.

There is no plug-and-play solution for this project in the way that mRNA vaccines were perfectly set up for SARS-CoV-2. We have no such technology to immediately redeploy here, he said. Were going to have to reimagine what it means to be a gene therapy for this project.

Excerpt from:
Novartis, Gates Foundation pursue a simpler gene therapy for sickle cell - STAT

Newswise PHILADELPHIAScientists in the Perelman School of Medicine at the University of Pennsylvania have uncovered the molecular causes of a congenital form of dilated cardiomyopathy (DCM), an often-fatal heart disorder.

This inherited form of DCM which affects at least several thousand people in the United States at any one time and often causes sudden death or progressive heart failure is one of multiple congenital disorders known to be caused by inherited mutations in a gene called LMNA. The LMNA gene is active in most cell types, and researchers have not understood why LMNA mutations affect particular organs such as the heart while sparing most other organs and tissues.

In the study, published this week in Cell Stem Cell, the Penn Medicine scientists used stem cell techniques to grow human heart muscle cells containing DCM-causing mutations in LMNA. They found that these mutations severely disrupt the structural organization of DNA in the nucleus of heart muscle cells but not two other cell types studied leading to the abnormal activation of non-heart muscle genes.

Were now beginning to understand why patients with LMNA mutations have tissue-restricted disorders such as DCM even though the gene is expressed in most cell types, said study co-senior author Rajan Jain, MD, an assistant professor of Cardiovascular Medicine and Cell and Developmental Biology at the Perelman School of Medicine.

Further work along these lines should enable us to predict how LMNA mutations will manifest in individual patients, and ultimately we may be able to intervene with drugs to correct the genome disorganization that these mutations cause, said study co-senior author Kiran Musunuru, MD, PhD, a professor of Cardiovascular Medicine and Genetics, and Director of the Genetic and Epigenetic Origins of Disease Program at Penn Medicine.

Inherited LMNA mutations have long puzzled researchers. The LMNA gene encodes proteins that form a lacy structure on the inner wall of the cell nucleus, where chromosomes full of coiled DNA are housed. This lacy structure, known as the nuclear lamina, touches some parts of the genome, and these lamina-genome interactions help regulate gene activity, for example in the process of cell division. The puzzle is that the nuclear lamina is found in most cell types, yet the disruption of this important and near-ubiquitous cellular component by LMNA mutations causes only a handful of relatively specific clinical disorders, including a form of DCM, two forms of muscular dystrophy, and a form of progeria a syndrome that resembles rapid aging.

To better understand how LMNA mutations can cause DCM, Jain, Musunuru, and their colleagues took cells from a healthy human donor, and used the CRISPR gene-editing technique to create known DCM-causing LMNA mutations in each cell. They then used stem cell methods to turn these cells into heart muscle cells cardiomyocytes and, for comparison, liver and fat cells. Their goal was to discover what was happening in the mutation-containing cardiomyocytes that wasnt happening in the other cell types.

The researchers found that in the LMNA-mutant cardiomyocytes but hardly at all in the other two cell types the nuclear lamina had an altered appearance and did not connect to the genome in the usual way. This disruption of lamina-genome interactions led to a failure of normal gene regulation: many genes that should be switched off in heart muscle cells were active. The researchers examined cells taken from DCM patients with LMNA mutations and found similar abnormalities in gene activity.

A distinctive pattern of gene activity essentially defines what biologists call the identity of a cell. Thus the DCM-causing LMNA mutations had begun to alter the identity of cardiomyocytes, giving them features of other cell types.

The LMNA-mutant cardiomyocytes also had another defect seen in patients with LMNA-linked DCM: the heart muscle cells had lost much of the mechanical elasticity that normally allows them to contract and stretch as needed. The same deficiency was not seen in the LMNA-mutant liver and fat cells.

Research is ongoing to understand whether changes in elasticity in the heart cells with LMNA mutations occurs prior to changes in genome organization, or whether the genome interactions at the lamina help ensure proper elasticity. Their experiments did suggest an explanation for the differences between the lamina-genome connections being badly disrupted in LMNA-mutant cardiomyocytes but not so much in LMNA-mutant liver and fat cells: Every cell type uses a distinct pattern of chemical marks on its genome, called epigenetic marks, to program its patterns of gene activity, and this pattern in cardiomyocytes apparently results in lamina-genome interactions that are especially vulnerable to disruption in the presence of certain LMNA mutations.

The findings reveal the likely importance of the nuclear lamina in regulating cell identity and the physical organization of the genome, Jain said. This also opens up new avenues of research that could one day lead to the successful treatment or prevention of LMNA-mutations and related disorders.

Other co-authors of the study were co-first authors Parisha Shah and Wenjian Lv; and Joshua Rhoades, Andrey Poleshko, Deepti Abbey, Matthew Caporizzo, Ricardo Linares-Saldana, Julie Heffler, Nazish Sayed, Dilip Thomas, Qiaohong Wang, Liam Stanton, Kenneth Bedi, Michael Morley, Thomas Cappola, Anjali Owens, Kenneth Margulies, David Frank, Joseph Wu, Daniel Rader, Wenli Yang, and Benjamin Prosser.

Funding was provided by the Burroughs Wellcome Career Award for Medical Scientists, Gilead Research Scholars Award, Pennsylvania Department of Health, American Heart Association/Allen Initiative, the National Institutes of Health (DP2 HL147123, R35 HL145203, R01 HL149891, F31 HL147416, NSF15-48571, R01 GM137425), the Penn Institute of Regenerative Medicine, and the Winkelman Family Fund for Cardiac Innovation.

###

Penn Medicineis one of the worlds leading academic medical centers, dedicated to the related missions of medical education, biomedical research, and excellence in patient care. Penn Medicine consists of theRaymond and Ruth Perelman School of Medicine at the University of Pennsylvania (founded in 1765 as the nations first medical school) and theUniversity of Pennsylvania Health System, which together form a $8.6 billion enterprise.

The Perelman School of Medicine has been ranked among the top medical schools in the United States for more than 20 years, according toU.S. News & World Report's survey of research-oriented medical schools. The School is consistently among the nation's top recipients of funding from the National Institutes of Health, with $494 million awarded in the 2019 fiscal year.

The University of Pennsylvania Health Systems patient care facilities include: the Hospital of the University of Pennsylvania and Penn Presbyterian Medical Centerwhich are recognized as one of the nations top Honor Roll hospitals byU.S. News & World ReportChester County Hospital; Lancaster General Health; Penn Medicine Princeton Health; and Pennsylvania Hospital, the nations first hospital, founded in 1751. Additional facilities and enterprises include Good Shepherd Penn Partners, Penn Medicine at Home, Lancaster Behavioral Health Hospital, and Princeton House Behavioral Health, among others.

Penn Medicine is powered by a talented and dedicated workforce of more than 43,900 people. The organization also has alliances with top community health systems across both Southeastern Pennsylvania and Southern New Jersey, creating more options for patients no matter where they live.

Penn Medicine is committed to improving lives and health through a variety of community-based programs and activities. In fiscal year 2019, Penn Medicine provided more than $583 million to benefit our community.

See the original post here:
Stem Cell Study Illuminates the Cause of a Devastating Inherited Heart Disorder - Newswise

Apart from new findings on coronavirus every single day, the year was also filled with stories from outer space, archeology and anatomy

The year 2020 also termed as the year of the pandemic, social distancing, work from home, was also the year of research at breakneck speed. Virologists, immunologists, computational biologists, epidemiologists, and medical professionals across the globe turned into superheroes without capes.

Quick sequencing of the whole genome of the novel coronavirus (SARS-CoV-2) helped develop various test kits. We now have not one or two, but multiple COVID-19 vaccines that have succeeded in human clinical trials. Moderna's and Pfizer-BioNTechs vaccines that use messenger RNA have reported efficacy of about 95%, and the United Kingdom, the United States and the United Arab Emirates have already launched mass vaccinations.

Apart from new findings on coronavirus every single day, the year was also filled with stories from outer space, archeology and anatomy. Here is a list of a few of them in random order

In October, NASA confirmed, for the first time, water on the sunlit side of the Moon indicating that water may be distributed across the moons surface, and not limited to the cold and shadowed side.

Researchers from the Netherlands Cancer Institute announced in October that they have discovered a new pair of salivary glands hidden between the nasal cavity and throat. The team proposed the name tubarial glands and noted that this identification could help to explain and avoid radiation-induced side-effects such as trouble during eating, swallowing, and speaking.

In September, an international scientific team announced that they have spotted phosphine gas on Venus. On Earth, microorganisms that live in anaerobic (with no oxygen) environments produce phosphine. Massachusetts Institute of Technology molecular astrophysicist and study co-author Clara Sousa-Silva said in a release, This is important because, if it is phosphine, and if it is life, it means that we are not alone. It also means that life itself must be very common, and there must be many other inhabited planets throughout our galaxy.

Read our detailed explainer here.

In March, a person suffering from Leber congenital amaurosis, a rare inherited disease that leads to blindness, became the first to have CRISPR/Cas-9-based therapy directly injected into the body.

In June, two patients with beta-thalassemia and one with sickle cell disease had their bone marrow stem cells edited using CRISPR techniques.

Click here to read our explainer on the genome-editing tool that won this years Nobel Prize for Chemistry.

The year 2020 marks 100 years of discovery of Indus Valley Civilisation, and a new study showed that dairy products were being produced by the Harappans as far back as 2500 BCE.

Another study found the presence of animal products, including cattle and buffalo meat, in ceramic vessels dating back about 4,600 years.

Chinas Change-5 probe brought back about 1,731 grams of samples from the moon becoming the third country to bring moon samples after the U.S and Soviet Union.

Also, Japans Hayabusa 2 brought back the first extensive samples from an asteroid. The spacecraft, launched from Japan's Tanegashima space centre in 2014, took four years to reach the asteroid Ryugu before taking a sample and heading back to Earth in November 2019.

Mars rover Perseverance blasted off for the red planet on July 30 to bring the first Martian rock samples back to Earth. If all goes well, the rover will descend to the Martian surface on February 18, 2021.

You have reached your limit for free articles this month.

Find mobile-friendly version of articles from the day's newspaper in one easy-to-read list.

Enjoy reading as many articles as you wish without any limitations.

A select list of articles that match your interests and tastes.

Move smoothly between articles as our pages load instantly.

A one-stop-shop for seeing the latest updates, and managing your preferences.

We brief you on the latest and most important developments, three times a day.

Support Quality Journalism.

*Our Digital Subscription plans do not currently include the e-paper, crossword and print.

Read the original here:
2020: The year science took centre-stage - The Hindu

Covid-19 sucked most of the oxygen out of science this year. But we still had brilliant wins.

The pandemic couldnt bring rockets or humans down: multiple missions blasted off to the red planet in the summer of Mars. Two astronauts launched to the International Space Stationand made it safely backin a game-changer for commercial space travel. NASA released dozens of findings on how space travel changes our bodies, paving the way to keep us healthy in orbitor one day, on Mars and beyond.

Back on Earth, scientists scoured mud ponds and fished out a teeny-tiny CRISPR enzyme that packs a massive punch for genome editing. AI and neuroscience became even more entwinedsometimes literally. Biological neurons got hooked up to two silicon-based artificial neurons, across multiple countries, into a fully-functional biohybrid neural network. Others tapped dopaminethe main messenger for the brains reward systemto unite electricity and chemical computing into a semi-living computer. While still largely a curiosity, these studies take brain-inspired computers to another level by seamlessly incorporating living neurons into AI hardware. Now imagine similar circuits inside the brainNeuralink sure is.

More abstractly, biological and artificial brains further fed into each other in our understandingand craftingof intelligence. This year, scientists found mini-computers in the input tree-like branches of neurons. Like entire neural networks, these cables were capable of performing complex logical calculations, suggesting our brain cells are far brainier than we previously thoughtsomething AI can learn from. On the flip side, a hotshot algorithm inspired by the brain called reinforcement learning pushed neuroscientists to re-examine how we respond to feedback as we learn. AI also helped build the most dynamic brain atlas to date, a living map that can continuously incorporate new data and capture individual differences.

As we leave 2020 behind, two main themes percolate in my mind, not just for what theyve accomplished, but as indicators of what lies ahead. These are the trends Ill be keeping my eyes on in the coming year.

Why we age is extremely complex. So are methods that try to prevent age-related diseases, or slow the aging process itself. This nth-dimensional complexity almost dictates that longevity research needs to self-segregate into lanes.

Take probing the biological mechanisms that drive aging. For example, our cells energy factory spews out bullet-like molecules that damage the cell. The genome becomes unstable. Cells turn zombie-like. Working stem cells vanish. Tissue regeneration suffers. Scientists often spend entire careers understanding one facet of a single hallmark of aging, or hunting for age-related genes. The lucky ones come up with ways to combat that one foefor example, senolytics, a family of drugs that wipe out zombie cells to protect against age-related diseases.

But aging hallmarks dont rear their heads in isolation. They work together. An increasing trend is to unveil the how of their interactions workcrosstalk, in science-speakwith hopes of multiple birds with one stone.

This year, longevity researchers crossed lanes.

One study, for example, took a stem cell playbook to rejuvenate eyesight in aged mice with vision loss. They focused on a prominent aging hallmark: epigenetics. Our DNA is dotted with thousands of chemical marks. As we age, these marks accumulate. Using gene therapy, the team introduced three superstar genes into the eyes of aged mice to revert those marks and reprogram cells to a younger state. Youve probably heard of those genes: theyre three of the four factors used to revert adult skin cells into a stem-cell-like state, or iPSCs (induced pluripotent stem cells). Resetting the epigenetic clock was so powerful it improved visual acuity in old mice, and the team has now licensed the tech to Life Biosciences in Boston to further develop for humans.

Another study combined three main puzzle pieces in agingzombie cells, inflammation, and malfunctioning mitochondriainto a full picture, with the surprise ending that senolytics has multiple anti-aging powers in cells. Talk about killing two birds with one stone. Finally, one team (which I was a part of) combined two promising approaches for brain rejuvenationexercise and young bloodto begin pushing the limits of reigniting faltering memory and cognition due to aging.

Longevity research has long been fragmented, but its starting to coalesce into a multidisciplinary field. These crossovers are just the start of a rising trajectory to combat the multi-headed Hydra thats aging. More will come.

If youre looking for a sign that AI is leaving the digital realm of Atari games and heading into the real world, this year was it.

In biotech, theres no doubt of AIs promise in drug discovery or medical diagnoses. In late 2019, a team used deep learning and generative modelssimilar to AlphaGo, the DeepMind algorithm that trounced humans at Go and wiped the Atari libraryto conjure over 30,000 new drug molecules, a feat chemists could only dream of. This year, the viral hurricane thats Covid-19 further unleashed AI-based drug discovery, such as screening existing drugs for candidates that may work against the virus, or newlydesigned chemicals to fight off SARS-CoV-2 infectionthe virus that causes Covid-19.

For now, we dont yet have an AI-designed drug on the market, an ultimate test for the technologys promise. However, although AI wasnt able to make a splash in our current pandemic battle, the scene is set for tackling the next oneand drug discovery as a whole.

In contrast, AI-based medical diagnosis had a resounding win. This year, the FDA approved a software that uses AI to provide real-time guidance for ultrasound imaging for the heart, essentially allowing those without specialized training to perform the test. The approval brings a total of 29 FDA-approved AI-based medical technologies to date. Even as the debate on trust, ethics, and responsibility for AI doctors cranked up in temperature, the Pandoras box has been opened.

Medicine aside, deep learning further honed its craft in a variety of fields. The neuroscience-AI marriage is one for the ages with no signs of fracture. Outside the brain, AI also gave synthetic biology a leg up by parsing the interactions between genes and genetic networksa mind-bending, enormously complex problem previously only achieved through trial and error. With help from AI, synthetic biologists can predict how changes to one gene in a cell could affect others, and in turn, the cells biochemistry and behavior. Bottom line: it makes designing new biological circuits, such as getting yeast to pump out green fuels or artificially hoppy beer, much easier.

But the coup de grce against AI as an overhyped technology is DeepMinds decimation of a 50-year-long challenge in biology. With a performance that shocked experts, DeepMinds AlphaFold was able to predict a proteins 3D structure from its amino acid sequencethe individual components of a proteinmatching the current gold standard. As the workhorses of our bodies, proteins dictate life. AlphaFold, in a sense, solved a huge chunk of the biology of life, with implications for both drug discovery and synthetic biology.

One more scientific brilliance this year is the use of light in neuroscience and tissue engineering. One study, for example, used lasers to directly print a human ear-like structure under the skin of mice, without a single surgical cut. Another used light to incept smell in mice, artificially programming an entirely new, never-seen-in-nature perception of a scent directly into their brains. Yet another study combined lasers with virtual reality to dissect how our brains process space and navigation, mentally transporting a mouse to a virtual location linked to a reward. To cap it off, scientists found a new way to use light to control the brain through the skull without surgerythough as of now, youll still need gene therapy. Given the implications of unauthorized mind control, thats probably less of a bug and more of a feature.

Were nearing the frustratingly slow, but sure, dying gasp of Covid-19. The pandemic defined 2020, but science kept hustling along. I cant wait to share what might come in the next year with youmay it be revolutionary, potentially terrifying, utterly bizarre* or oddly heart-warming.

* For example, Why wild giant pandas frequently roll in horse manure. Yes thats the actual title of a study. Yes, its a great read. And yes, its hilarious but has a point.

Image Credit: Greyson Joralemon on Unsplash

Read more:
2020 in Neuroscience, Longevity, and AIand What's to Come - Singularity Hub

CAMBRIDGE, Mass., Dec. 05, 2020 (GLOBE NEWSWIRE) -- Intellia Therapeutics, Inc. (NASDAQ:NTLA), is presenting new preclinical data in support of NTLA-5001, the company’s wholly owned Wilms’ Tumor 1 (WT1)-directed T cell receptor (TCR)-T cell therapy candidate for the treatment of acute myeloid leukemia (AML), at the 62nd American Society of Hematology (ASH) Annual Meeting, taking place virtually from December 5-8, 2020. NTLA-5001 capitalizes on how natural T cells recognize and respond to tumors. The target, WT1, is highly overexpressed in AML, a cancer of the blood and bone marrow that is often fatal despite existing treatments (NIH SEER Cancer Stat Facts: Leukemia – AML). The new preclinical data being presented today highlight the faster expansion and superior function of T cells manufactured by Intellia’s proprietary approach, compared to a standard genome editing process. Specifically, NTLA-5001’s lead TCR-T cells resulted in significantly higher anti-tumor activity in mouse models of acute leukemias than that observed in mice treated with cells engineered using the standard process.

Read more:
Intellia Therapeutics Presents New Preclinical Data Supporting Its CRISPR/Cas9-Engineered TCR-T Cell Treatment for Acute Myeloid Leukemia at the...

Detroit Lions senior VP of business development Kelly Kozole works with her daughter, Morgan, who has a rare neurological disorder called beta-propeller protein-associated neurodegeneration, or BPAN.Michael Rothstein

TROY, Mich. -- Wearing a white T-shirt with a massive star in sparkling shades of pink, yellow and seafoam green on the front, Morgan Kozole sits in front of a fold-up chalkboard in the living room of her family's Detroit-area home and starts to draw.

Using pink and yellow chalk, she sketches Mickey and Minnie Mouse. The Disney characters are dominant fixtures in the 5-year-old's life and therefore become a soundtrack for the Kozole family: Morgan constantly saying "Mickey," with her long, blond ponytail bouncing to whatever song happens to be playing on the Mickey Mouse Club.

"These are the two Mickeys," Morgan says, pointing to the chalkboard. Her mother, Detroit Lions senior vice president of business development Kelly Kozole, explains that this is her way of communicating that she would like a visitor to draw Mickey too. If it's close, Morgan accepts it. Another Mickey to fawn over.

For Morgan's birthday earlier this year, the family went to Disney World. On this trip, the Kozoles saw what they had longed for: the potential of progress.

"She knew where we were. She knew Mickey Mouse," Kelly said. "Before, she wouldn't go to the characters, and now she's jumping up and down, hugging. She really, along those lines, is also really into birthdays.

2 Related

"The 'Happy Birthday' song. Before that, she was just kind of looking. Sometimes it was too much for her with everyone singing -- sometimes loud noises are too much. This year, we had to sing 'Happy Birthday' to her three times."

Birthdays, for children, are happy occasions -- reasons for grand celebrations of progress toward adulthood. For the rest of Morgan's family it is more complicated.

Morgan has a rare neurological disease called beta-propeller protein-associated neurodegeneration, known as BPAN. It's a disorder, more prevalent in girls than boys, that causes delayed development and seizures, communication issues and, sometimes, motor dysfunction. It's unclear exactly how many people are living with BPAN worldwide due to its rarity, although Dr. Sami Barmada, a scientist at the University of Michigan studying BPAN, estimates roughly 500 to 600 people.

It's rare enough that Dr. Henry Paulson, the director of the Michigan Alzheimer's Disease Center, said there are experts in neurodegeneration who are unfamiliar with BPAN. While Kelly is trying to advocate for her daughter and others with BPAN through fundraising for research, science moves only so fast.

The Kozoles understand that. So birthdays for the family aren't always happy. They are a reminder of what could come.

"That ticking time clock," Kelly said. "Every birthday isn't exciting for me for her. Because it's one year closer to when this bomb is going to go off."

BPAN's rarity makes the reality heartbreakingly simple: There are very few effective treatments, little research and no cure. As Morgan learns how to organize her Peppa Pig characters and learns new words on her iPad -- her future looms.

At some unpredictable point in Morgan's teen and adult years -- the average is around age 25, according to Barmada -- development will just stop. Progress will decline and, in some cases, disappear. Those afflicted with BPAN begin suffering from progressive dystonia parkinsonism -- making it difficult to walk, talk or stand.

"Any day," Kelly said, "it could be like, 'Oh, your daughter's gone.'"

WHEN MORGAN WAS born on Jan. 12, 2015, she was, largely, a healthy baby. She was a little jaundiced but nothing worrisome.

When she would go to the doctor's office for shots, Morgan didn't cry. It was a little abnormal, but when you're a parent of a young child, no crying is viewed as a minor miracle. Kelly and her husband, Kevin, took this as a sign of a tough kid. Nurses even said how great it was.

Looking back, it was a warning sign that something was wrong. BPAN causes a high pain tolerance. Before long, more concerns popped up. Morgan wasn't crawling at nine months, wasn't walking at a year. Expected milestones passed without Morgan reaching them. Kevin and Kelly put her in therapy in late 2016 to work up to these childhood progressive traits and began researching potential causes. They wouldn't find an answer for more than two years.

"She was diagnosed with cerebral palsy at first. One doctor diagnosed her with that, and then another, our neurologist, said she doesn't have that," Kelly said. "Then there was speculation but not a full diagnosis she had autism, so we did all the tests for that.

"So through this kind of journey of trying to find out what was wrong, it was exciting that she didn't have something that you were going to this test for, but you still had so many more questions as you were eliminating all these potential diseases that she could have."

Befuddled, they began genetic testing and in November 2018 received a letter about a mutation on Morgan's WDR45 gene. Kelly Googled it, stumbled upon BPAN and freaked out, calling their neurologist. The neurologist told Kelly not to worry -- BPAN was very rare, and Morgan didn't have it.

Doctors diagnosed her with epilepsy because of seizures. Morgan took Keppra, which helped accelerate her vocabulary to about 50 words, typical for a 1-year-old, when she was 3. Then doctors said no, it wasn't epilepsy either.

Here's how the postseason bracket looks at the moment and what scenarios lie ahead. Playoff picture (ESPN+) Playoff Machine: See scenarios Standings | Football Power Index

Another meeting with another neurologist led to a different diagnosis. Three days after she and Kevin returned to Michigan from Super Bowl LIII in February 2019, they received a call. Doctors figured out what was wrong.

It was BPAN.

"In my mind, it's worse than cancer," Kelly said. "How is this even possible? That this can even be so painful for kids later on in life. You try so hard to gain all these abilities, and then early adolescence or early adulthood, it's just [gone] one day, and I've seen a lot of these stories.

"There's a BPAN Facebook website, and that's where the doctors sent us. There's no cure. There's no therapy. 'Go to this website.' That's what I was told."

FOR MONTHS KELLY cried, angry and heartbroken. The Kozoles initially told their families and no one else.

In May 2019, Kelly went to her first Neurodegeneration with Brain Iron Accumulation (NBIA) conference. She met other parents, heard their stories and began the new normal.

She used her skills -- organization, fundraising and business -- to brainstorm ways to help. Hardly anyone had researched BPAN. Without it, there would be no chance for a cure -- not in Morgan's lifetime, which could reach her 40s, and not in the lifetime of those who might come after.

She shared what was happening with her boss, Detroit Lions president Rod Wood, and his wife, Susan, using a website link to explain BPAN. Wood knew something was wrong because of texts and emails saying they had to take Morgan to this specialist or that appointment.

"As that was confirmed and became her reality, she is now able to talk about it, in a way," Wood said. "Because she's full bore on trying to help generate awareness and financial resources to find a cure for it.

"She went from the unknown to the very tragic known to, 'OK, what are we going to do about it?'"

Kelly consulted her aunts, both of whom worked in medicine. Linda Narhi worked in biotechnology for Amgen for more than 30 years; Dr. Diane Narhi was the first female chief of staff at Simi Valley (California) Hospital. From talking with another group of fundraising BPAN parents -- BPAN Warriors -- Kelly found a guide.

If her aunts had not been resources, she might have joined BPAN Warriors. But Kelly admittedly needs to be in control, and this was her daughter. She needed to manage this herself. She created a nonprofit called Don't Forget Morgan.

Kelly's aunts provided guidance, and Wood offered contacts he had in the finance industry and Silicon Valley. Wood and Lions general counsel Jay Colvin sit on the board. Other Lions coworkers -- with Wood's blessing -- built the website, designed the logo and created social media plans and the first pitch video for Don't Forget Morgan's rollout in 2020.

Everything you need this week: Full schedule | Standings Depth charts for every team Transactions | Injuries Football Power Index rankings More NFL coverage

Progress started with a $15,000 grant to help with a mouse model study at Sanford Research in South Dakota, with another, larger, potential grant to come. In recent months, Kelly has focused largely on fundraising, and another parent of a child with BPAN, Christina Mascarenhas Ftikas, has focused on the medical side of the nonprofit.

"This is why I'm here," Kelly said. "I'm supposed to be a vehicle to get all of this awareness and hopefully a cure for BPAN so the child one, two, three, five years from now, there is hope.

"There is no, 'Go to Facebook.' There is something where you can actually give a parent, 'Here's the symptoms to look for.'"

ABOUT AN HOUR away in Ann Arbor, Michigan, Kaci Kegler and her husband, Brian, had been in the same Facebook community. Kelly, new to the group and looking for a nearby connection, wrote Kaci a message.

"Hey, my daughter was just diagnosed, could we connect?"

Kaci understood. She did the same thing, reaching out without success in 2016 after her daughter, Elle, was diagnosed. Kaci wanted to be a resource.

They talked for an hour. There wasn't much Kaci could say to soothe her. Kelly pinged a year later with another message: I'm starting a nonprofit. Kaci offered to help.Despite suffering from BPAN, Morgan is like any other 5-year-old who enjoys playing with her brother, Connor.Michael Rothstein

Days later, on Feb. 28, Kaci and her husband, Brian, an assistant athletic director for development at the University of Michigan, had their yearly fundraiser for BPAN research on Rare Disease Day at Pizza House in Ann Arbor. They met a doctor who had a connection to researchers at Michigan.

"I literally came home and texted [Kelly] and was like, 'Oh my gosh, we may have inroads,'" Kaci said. "We just started texting. I have never met Kelly face-to-face. We still haven't. But we've texted a lot and we've emailed quite a bit.

"It just kind of started."

By summer, they went from nothing to putting pieces in place for a full-fledged research project with a two-year, $140,000 grant for Barmada and Dr. Jason Chua to help start to solve BPAN.

Chua was working on the regulation of autophagy, which is the cleaning out of damaged cells, and studying BPAN became a natural extension of the work he had already been putting in. BPAN alters that in neurons. Barmada said Chua's research provided a "rare win-win situation" to potentially help with BPAN and other diseases too.

"There are a set of questions in BPAN that nobody has the answer to," Barmada said. "And Jason and myself, we just seem to be in the right position, the right place to be able to help out."

The goal is to understand what is happening within BPAN itself and how people end up with it, while also trying to find therapies for existing patients. Within a year, they are hoping to grow stem cells from people with BPAN in their lab, allowing for the creation of their own stem cells missing the WDR45 gene. Then they will try to either replace the gene or "stimulate autophagy through genetic or pharmacologic means," Barmada said. The hope is this can prevent neurodegeneration.

So far, they've hired a research assistant to work with Chua, developed tools to manipulate the gene using the genome-editing tool CRISPR and applied for approval from Michigan and the institutional review board to get skin biopsies to obtain stem cells from BPAN patients.

It's a process, but it's also a start.

When RGIII was like Mike Vick in 2012 Cards' Kingsbury knew he wasn't Brady Colts rookies surging to head of class Bolts' Ekeler discusses hamstring tear Should Jets shut down Sam Darnold?

After partnering with Michigan and Sanford, Don't Forget Morgan also began working with Dr. Kathrin Meyer, a researcher at the Center for Gene Therapy at Nationwide Children's Hospital at Ohio State.

"Solving this disease is going to require more than Jason and Sami," Paulson said. "It's going to be a first shot across the bow, but it's going to require more than that. I'll say this, being in the field for a long time. Scientists who are coming up the pike say they want to look at Alzheimer's, want to look at epilepsy. They don't say, 'I want to look at a rare disease.'

"The only way to solve a rare disease is to get someone hooked. Sometimes when you hook a really good one, as I think we have with Jason here, you hook them for life and they make a difference."

MORGAN IS BOUNCING around the Kozoles' suburban Detroit home on this late August day. They just returned from northern Michigan, and having two kids, especially one with special needs, makes tidiness unrealistic.

COVID-19 changed things. Morgan hadn't been to many of her therapies for months. Online school barely kept her attention. There was concern she would have regression in her learning. Instead, her speech advanced by being around Kelly, Kevin and her older brother, Connor, all day. She has sung more songs recently to help increase her vocabulary. Sometimes, she'll listen 20 times in a row.

"Even more than that," Connor said. They aren't sure how much she's truly learning versus memorization. But it is something.Morgan Kozole has inspired her mother, Detroit Lions VP Kelly Kozole, to marshal researchers and other advocates to develop a cure for BPAN, and perhaps help future generations of children who live with the disorder.Michael Rothstein

The family gathers inside Morgan's bedroom -- complete with a special Haven Bed with a zipper to keep her safe from wandering around at night, when she could accidentally turn on the stove and hurt herself or others -- sleep disorders are another BPAN issue. She sits on the floor and starts playing with her small, yellow dollhouse and a fake ice-cream maker. Kelly asks for an ice cream. Morgan makes one for herself instead and pretends to eat it.

Later, outside, Morgan kicks a soccer ball and plays a modified game of catch with a squishy football. Football, no surprise, is big. She says "hike" a lot. "She knows that term," Kevin says, laughing.

In these moments, Morgan seems like any other young child. She attends St. Hugo of the Hills Parish School in Bloomfield Hills, Michigan, but has a one-on-one para nanny to help. She interacts with people, often overly affectionate.

Sitting at the kitchen table after playtime outside, she plays with Starfall, a children's learning app, on her iPad. They hope it accelerates her word recognition. Morgan is entranced watching "Farmer in the Dell" and using her hands to eat orange slices and Cheerios. She needs a mirror in front of her to provide her a target for her mouth. She listens to books, another way to try absorbing information.

Morgan can now count to 20 and say three sentences in a row. Kelly and Kevin have tried to give Morgan a normal life in an abnormal situation, but they worry about the future -- what she won't have and won't be able to experience.

But Morgan has changed some of that outlook too.

"Focus on how she is so loving and has so much pure joy. A lot of parents of special needs [kids] say you can learn so much from these kids, and you really can," Kelly said. "She is, every morning, just so happy, and 'Mama!' Hugs and kisses to strangers. She has none of those behaviors you learn as an adult where you're not kind to people or you don't want to talk to someone.

"She is just open arms, will give you a hug and is so loving, and it's like, 'Wow, this is really what life is about.'"

Go here to read the rest:
'This is why I'm here': A Detroit Lions VP tries to save her daughter from rare disease - ESPN

Egg cells harvested from Mauritian cynomolgus macaques (top left) were fertilized (top right) and injected with CRISPR gene editing materials to insert a genetic mutation that cured two men of HIV in the last decade. The growing embryos (developing in the bottom images), if carried to maturity by surrogates, will help researchers study the mutation as a potential treatment for HIV. Courtesy of Golos and Slukvin labs

A gene that cured a man of HIV a decade ago has been successfully added to developing monkey embryos in an effort to study more potential treatments for the disease.

Timothy Brown, known for years as the Berlin Patient, received a transplant of bone marrow stem cells in 2007 to treat leukemia. The cells came from a donor with a rare genetic mutation that left the surfaces of their white blood cells without a protein called CCR5. When Browns immune system was wiped out and replaced by the donated cells, his new immune systems cells carried the altered gene.

This mutation cuts a chunk out of the genome so that it loses a functional gene, CCR5, that is a co-receptor for HIV, says Ted Golos, a University of WisconsinMadison reproductive scientist and professor of comparative biosciences and obstetrics and gynecology. Without CCR5, the virus cant attach to and enter cells to make more HIV. So, in Timothy Browns case, his infection was eliminated.

In 2019, a second cancer patient Adam Castillejo, initially identified as the London patient was cleared of his HIV by a stem cell transplant conferring the same mutation.

Thats very exciting, and there have been some follow up studies. But its been complicated, to say the least, Golos says.

Between the two transplants came a more infamous application of the mutation, when in 2018 Chinese biophysicist He Jiankui announced he had used the DNA-editing tool CRISPR to write the mutation into the DNA of a pair of human embryos. His work drew criticism from scientists concerned with the ethics of altering genes that can be passed down to human offspring, and he was jailed by the Chinese government for fraud.

The promise of the CCR5 mutation remains, but not without further study. The mutation occurs naturally in fewer than 1 percent of people, suggesting that it may not be associated only with positive health outcomes. An animal model for research can help answer open questions.

Given interest in moving forward gene-editing technologies for correcting genetic diseases, preclinical studies of embryo editing in nonhuman primates are very critical, says stem cell researcher Igor Slukvin, a UWMadison professor of pathology and laboratory medicine.

Golos, Slukvin and colleagues at UWMadisons Wisconsin National Primate Research Center and schools of Veterinary Medicine and Medicine and Public Health employed CRISPR to edit the DNA in newly fertilized embryos of cynomolgus macaque monkeys. They published their work recently in the journal Scientific Reports.

Slukvins lab had already established a method for slicing the CCR5-producing gene out of the DNA in human pluripotent stem cells, which can be used to generate immune cells resistant to HIV.

We used that same targeting construct that we already knew worked in cells, and delivered it to one-cell fertilized embryos, says Jenna Kropp Schmidt, a Wisconsin National Primate Research Center scientist. The thought is that if you make the genetic edit in the early embryo that it should propagate through all the cells as the embryo grows.

Primate Center scientist Nick Strelchenko found that as much as one-third of the time the gene edits successfully deleted the sections of DNA in CRISPRs crosshairs base pairs in both of the two copies of the CCR5 gene on a chromosome and were carried on into new cells as the embryos grew.

The goal now is to transfer these embryos into surrogates to produce live offspring who carry the mutation, Schmidt says.

Cynomolgus macaques are native to Southeast Asia, but a group of the monkeys has lived in isolation on the Indian Ocean island of Mauritius for about 500 years. Because the entire Mauritian monkey line descends from a small handful of founders, they have just seven variations of the major histocompatibility complex, the group of genes that must be matched between donor and recipient for a successful bone marrow transplant. There are hundreds of MHC variations in humans.

With MHC-matched monkeys carrying the CCR5 mutation, the researchers would have a reliable way to study how successful the transplants are against the simian immunodeficiency virus, which works in monkeys just like HIV does in humans.

Anti-retroviral drugs have really positively changed the expectation for HIV infection, but in some patients, they may not be as effective. And theyre certainly not without long-term consequences, says Golos, whose work is funded by the National Institutes of Health. So, this is potentially an alternative approach, which also allows us to expand our understanding of the immune system and how it might protect people from HIV infection.

The animal model could lead to the development of gene-edited human hematopoietic stem cells the type that work in bone marrow to produce many kinds of blood cells that Slukvin and Golos say could be used as an off-the-shelf treatment for HIV infection.

This research was supported by grants from the National Institutes of Health (R24OD021322, P51OD011106, K99 HD099154-01, RR15459-01 and RR020141-01).

Follow this link:
Gene-edited monkey embryos give researchers new way to study HIV cure - University of Wisconsin-Madison

Emmanuelle Charpentier and Jennifer Doudna have scooped the 2020 Nobel prize in chemistry for the development of a method for genome editing. Specifically, theyve been awarded the prize for their discovery of the CrisprCas9 genome editing technique that allows scientists to make precise alterations to the genetic code of living organisms. CrisprCas9 is a powerful tool that could revolutionise many aspects of our lives, from medical treatments to the way we produce food. Its also seen its fair share of controversy in recent years. Here, we take a deeper look at these genetic scissors and why theyve won the Nobel prize.

Since Charpentier and Doudna began investigating the CrisprCas9 system in 2011, the field has exploded. Due to the relative simplicity and affordability of Crispr systems, researchers around the world have been able to apply the tools to all manner of different problems. Today there are entire journals, conferences and companies dedicated to the technique.

The ability to cut any DNA molecule at a chosen site has huge potential from treating genetic illnesses to creating disease-resistant crops. Trials have even shown how Crispr-delivered genetic modifications can spread through populations of mosquitoes and stop malaria infections such gene-drives offer a way to eliminate the disease altogether. And in the face of the Covid-19 pandemic, researchers have found ways to use Crispr in rapid coronavirus diagnostic tests and have also proposed using it to attack the viruss genome.

As Claes Gustafsson, chair of the Nobel committee for chemistry, said at the award announcement, There is enormous power in this genetic tool, which affects us all.

Crispr technology has even been used to make more delicious beer.

The whole Crispr gene editing tool has been adapted from the immune system of bacteria. The term Crispr comes from clustered regularly interspaced short palindromic repeats, which refers to distinct genetic sequences found in the genomes of bacteria. Each Crispr sequence is transcribed into RNA sequences that will target the DNA of a virus. These sequences also include cas (Crispr-associated) genes that code for DNA-cutting Cas enzymes. Together, the guide RNA and Cas enzyme form a complex that hunts out viral DNA and chops it up.

In Crispr gene editing, scientists repurpose this system by designing a guide RNA sequence of around 20 nucleobases that matches up to a DNA sequence they wish to target in a cells genome. This RNA sequence is paired with the Cas9 enzyme that will cut the DNA strand at the targeted site. The whole DNA sequence coding for both these components of the Crispr-Cas9 tool can be delivered to the target cell via a plasmid.

The tool can therefore be used to edit a cells genome with incredible precision for example, it can cut out a dysfunctional gene associated with a hereditary illness. And if the healthy version of the gene is also delivered to the cell, the cells own repair system will then incorporate the healthy strands at the site where it has been cleaved.

In 2011, when investigating the bacteria Streptococcus pyogenes, Charpentier discovered a molecule called tracrRNA that forms a key part of the CrisprCas system in bacteria.

Meanwhile, Doudna had been investigated the function of the cas genes, and learned that the Cas proteins they code for are involved in cutting up DNA as part of the bacterial immune system against pathogenic viruses.

That year Charpentier teamed up with Doudna to investigate the system further. Together they revealed how the Cas9 protein, CrisprRNA and tracrRNA worked together to snip DNA strands into two parts. They then simplified the system by combining the CrisprRNA and tracrRNA into a single molecule guide RNA making it easier to use, and showed how this could be used to cut any DNA strand at a site of their choosing, opening the door to using the tool in all manner of genome editing experiments.

While previous tools for genetic editing existed before Crispr-Cas9, the new tools are much simpler and cheaper. This has led to the huge expansion of the field by making gene editing accessible for scientists all around the globe.

For years Crispr has been at the centre of a long-running patent dispute. Shortly after Doudna and Charpentiers discovery, Feng Zhangs team the Broad Institute in Cambridge, US, patented a way to use the technique in eukaryotic cells. There have been protracted court battles between Doudnas group at the University of California in Berkeley, US, and the Broad team over who holds the key piece of intellectual property. In the meantime, numerous groups and companies have been granted patents for many new Crispr-related technologies, meaning that as time goes on, the original patents at the centre of the dispute are becoming less relevant.

Another area of controversy surrounds the potential consequences of using genome editing tools at all. As the genome is so complex, we cant always know what will happen when we edit genes. Some genes have multiple and often unknown functions editing them to correct for one problem could end up creating new unforeseen ones. This is particularly important when it comes to editing germline cells (those that can be passed on to an organisms children), because the modified genes can be inherited by future generations.

As a relatively new technique, we also know that Crispr itself isnt perfect. Some studies have shown off-target cuts, where the tool has snipped DNA strands at additional locations to the desired site. This clearly can have harmful consequences, and so many researchers are looking into ways to improve the technique and make it more suitable for medical uses.

With these concerns in mind, scientists worldwide including Doudna and Charpentier have called for a moratorium on editing human germline cells, until we can know more about the consequences. Such calls intensified after the rogue Chinese scientist He Jiankui edited human embryos that were then brought to term in 2018. He is now serving a three year prison sentence for conducting the study.

Several clinical trials have already begun on Crispr-based therapies, with promising reports emerging this year. In February, the first study to look at a cancer treatment using Crispr-edited immune cells reported that the modified cells were safe, with no serious side-effects in the three patients studied. While the efficacy of the treatment on the cancers was minimal, it may help to inform future Crispr-based T-cell treatments.

One month later, a patient with hereditary blindness became the first person ever to have a CrisprCas9 therapy directly administered into their body. And in June, the Swiss gene-editing company Crispr Therapeutics announced that two patients with beta thalassaemia and one with sickle cell disease would no longer require blood transfusions after their bone marrow stem cells were edited using Crispr techniques.

Earlier this week, Doudna launched a new company, Scribe Therapeutics, to begin work on treatments for amyotrophic lateral sclerosis.

Other Crispr-based technologies are coming closer to commercial reality. For example, the US genome engineering company eGenesis is developing ways to use the technique to edit pigs genes so that their organs might be transplanted safely into humans. In the agricultural sector, many companies are working on ways to use Crispr to speed up the selection process for crops with desirable traits such as disease-resistance or improved flavour.

At the fundamental level, researchers are working on ways to improve the system itself. By using alternative Cas proteins, some groups hope to make the tool more effective and easier to use in certain settings. Doudnas group recently reported on a CasX protein that is smaller than Cas9 and potentially easier to introduce into target cells.

Delivering DNA into cells and tissues is an important part of gene therapy, even more so for Crispr-Cas9 approaches because plasmids carrying this system are very large. This research paper describes a non-viral vector for delivering plasmid DNA carrying Crispr-Cas9 into tumour spheroids, which are good in vitro models for tissues but also challenging transfecting targets.

1 S J Zamolo, T Darbre and J-L Reymond, Transfecting tissue models with CRISPR/Cas9 plasmid DNA using peptide dendrimers, Chem. Commun., 2020, DOI: 10.1039/d0cc04750c

Regulating the function of Crispr-Cas9 is on the agenda for many researchers because the ability to restrict it in a spatial and temporal manner opens the door to precisely manipulating genomes and minimising any side effects. By introducing photolabile groups into the system, these researchers have shown how they can regulate Cas9 activity with light

2 Y Wang et al, Photocontrol of CRISPR/Cas9 function by site-specific chemical modification of guide RNA,Chem. Sci., 2020, DOI: 10.1039/d0sc04343e

It seems that Crispr-Cas systems arent just handy for gene editing. This paper describes how the Crispr-Cas system was used to assemble a multi-enzyme cascade containing five distinct enzymes. The team behind the work hope it could be the beginnings of a general method for building complex scaffolded biocatalytic pathways

3 S Lim et al, CRISPR/Cas-directed programmable assembly of multi-enzyme complexes, Chem. Commun., 2020, 56, 4950 (DOI: 10.1039/d0cc01174f)

And to round things off, here are some reviews on how Crispr-Cas9 works, the delivery processes for therapeutic nanoparticles and the physiological obstacles for those process

4 Y Xu, R Liu and Z Dai, Key considerations in designing CRISPR/Cas9-carrying nanoparticles for therapeutic genome editing, Nanoscale, 2020, DOI: 10.1039/d0nr05452f

5 Y Gong et al,Lipid and polymer mediated CRISPR/Cas9 gene editing, J. Mater. Chem. B, 2020,8, 4369 (DOI: 10.1039/d0tb00207k)

Excerpt from:
Explainer: What is Crispr and why did it win the Nobel prize? - Chemistry World

Yes, even your metabolism has a memory and it can hold a grudge for years. In people with diabetes, periods of high blood sugar can negatively impact their health years later, even if they get their blood sugar under control. While this metabolic memory phenomenon has been known for years, why it happens is poorly understood.

Rama Natarajan, Ph.D., Professor and Chair of the Department of Diabetes Complications & Metabolism at City of Hope, turned to our epigenome for the answer.

Weve shown the first link between DNA methylation in blood and stems cells, blood sugar history, and future development of complications, said Natarajan. This highlights the importance of good glycemic control to prevent long-term complications.

The history of metabolic memory

We now know high blood sugar can lead to a variety of complications, including eye disease, kidney disease, nerve problems, heart disease, and stroke. But the relationship between strict blood sugar control and complication risk wasnt well understood before the 1980s.

Back in 1983, the Diabetes Control and Complications Trial (DCCT) began tracking complications in 1,441 participants with type 1 diabetes. Researchers compared the occurrence of long-term complications between participants who tightly regulated their blood glucose levels to those who followed less strict standard regulation.

After 10 years, the difference was striking the risk of diabetic complications was reduced in participants who tightly regulated their blood sugar but not in those following standard regulation. In other words, a person with higher blood sugar had a higher risk of complications.

To continue following the DCCT patients, the Epidemiology of Diabetes Interventions and Complications (EDIC) follow-up trial began at the end of DCCT in 1993 and is ongoing. At the end of DCCT, all participants were encouraged to adopt strict blood sugar regulation; many in the standard regulation group did.

Despite blood sugar regulation being very similar in all the patients (as measured by hemoglobin A1c, called HbA1c), differences persisted between the two original intervention groups. The phenomenon of long-term effects from high or variable blood sugar control is called metabolic memory (or the legacy effect in type 2 diabetes).

Complications resulted from total high blood sugar exposure it didnt matter whether the person was exposed to slightly elevated levels over a long time or high levels over a short time.

So, what caused the sweet sugar molecule to become so destructive?

Sugary destruction

Extra sugar in your blood can interact with your cells, DNA, and proteins, adding itself onto things it shouldnt be on through a process called glycation. In fact, HbA1c can be thought of as sugar-coated red blood cells.

The sugar-coated molecules cant function as well, if at all, and the damage begins a self-perpetuating cycle. Not only do these damaged molecules stop working, they can also accumulate in the skin, eyes, and other organs, causing damage. Build-up of sugar-coated molecules can trigger the creation of harmful free radicals, causing oxidative stress and feeding a destructive cycle.

Although sugar can directly modify molecules, it can also trigger other epigenetic modifications. These modifications can control how genes are expressed, changing protein levels in cells.

There hasnt been a strong genetic association with diabetic complications very few genetic mutations have been strongly linked to complications, Natarajan explained. But we knew the epigenome is what makes identical twins different and can have implications into why one gets diabetes or cancer and the other doesnt. So, we turned our focus to epigenetics.

Epigenetics and diabetes

Natarajan sought to explain the long-term sugary destruction wrought by high blood sugar by searching the epigenome. Her lab specifically looks for one type of modification called DNA methylation, where a tiny molecule called a methyl group is added onto DNA.

Epigenetics is the coating on top of genetics that can be altered by environmental influences, Natarajan said. We started focusing on the role of epigenetics in developing diabetes and its complications because we know that lifestyles, improper diet, lack of exercise, and even viruses can affect epigenetics.

Natarajans lab began collaborating with the DCCT trial group, analyzing data collected through the trial for epigenetic clues to explain the metabolic memory of complications. They found more modifications associated with active genes on proteins called histones that are wrapped by DNA in participants with regular blood sugar control compared to the strict controllers. Even more interesting was that many epigenetic DNA methylation variations between the two groups persisted through at least 17 years of follow-up in the EDIC study.

These changes were in important genes related to complications, showing something about persistent epigenetic programming in peripheral blood cells, commented Natarajan. Previous high blood sugar episodes could be a key factor in why these genes were continually misbehaving.

Now, Natarajans lab illuminated even more links between epigenetic changes, blood sugar history, and metabolic memory in their recent Nature Metabolism paper. Persistent epigenetic modifications of a few key genes were detected in participants with previously less regulated blood sugar who developed either retinopathy or nephropathy. They showed that DNA methylation is a key link between a patients HbA1c history, metabolic memory, and development of future complications.

Many HbA1c-associated modifications were in stem cells and the blood cells they create. Even though blood cells are turned over relatively quickly, stem cells stick around for a long-time, so changes in stem cells can have long-term consequences.

The important thing we found was the connection to stem cells, explained Natarajan. Were asking how these changes alter inflammatory gene expression and how we can interrupt those pathways.

Sugar-modified genes arent so sweet

Natarajans lab sorted through all the modified genes to find the most common modifications in participants with less strict blood sugar control. The most commonly modified gene coded for thioredoxin-interacting protein (TxNIP).

TxNIP is not a new protein, but the discovery that its DNA methylation is altered by different glycemic control is new, Natarajan added.

Thioredoxin-interacting protein is known to be highly regulated in certain pancreas cells, called beta cells, that release insulin. The plot thickened when high blood sugar was found to increase TxNIP protein production. Even more interesting, high TxNIP protein levels make beta-cells dysfunctional, ultimately leading to their untimely death. So, high blood sugar triggers more TxNIP to be produced, possibly through epigenetic modifications of the TxNIP gene, which ultimately leads to the death of insulin-producing beta cells.

Showing that the TxNIP gene can be epigenetically modified for years and years suggests that it could be one of the culprits causing long-term problems in diabetes, Natarajan said.

The proteins that TxNIP interacts with, called thioredoxins, protect against oxidative stress. TxNIP can bind to and inactivate thioredoxin to increase oxidative stress by increasing reactive oxygen species (ROS). In mouse cells in a dish, high glucose exposure triggered increased ROS levels mediated by TxNIP, leading to oxidative stress. Oxidative stress can trigger cell and organ damage, so this could be one mechanism explaining diabetes-induced damage.

Her lab also found epigenetic changes in other genes related to inflammation and inflammation-related processes.

Next steps and clinical implications

Natarajans lab is continuing to study the link between blood sugar history, epigenetics, and other complications of diabetes. They are also expanding their scope, searching the entire genome for more epigenetic modifications linked with past blood sugar maintenance.

This study also lays the groundwork for further studies with meaningful clinical implications, including developing epigenetic biomarkers for diabetic complications. In the future, Natarajan says a simple blood test looking at key epigenetic modifications, along with HbA1c history, could be used to predict future risk of retinopathy, nephropathy, and neuropathy. This would allow the doctor to figure out who should have early and more aggressive treatment to mitigate complication risk.

While these studies were done in type 1 diabetes patients, other studies in type 2 diabetes patients have shown similar epigenetic modifications after history of higher blood sugar levels.

Turning knowledge into potential drugs

What about doing something about the epigenetic modifications can we remove them? As a matter of fact, yes!

There is an interesting new type of experimental drug on the horizon called epigenetic editing. The hot new technology CRISPR isnt just for cutting out chunks of DNA or controlling genes it can also be used to insert or remove epigenetic modifications. While this technology is still experimental and in early preclinical animal studies, the potential is very exciting.

A CRISPR/enzyme pair can be used the CRISPR genetic material can hunt down the genetic spot you want to change; and the attached enzyme can snip or add certain molecules to the DNA, effectively removing or creating an epigenetic modification, thereby activating or silencing the targeted gene.

Enzymes such as methyltransferase or demethylase can add or remove methyl groups from genes. Because they just change what is on the gene or histone wrapped around it (not the genetic sequence itself), the gene itself isnt tampered with, meaning there could be less genetic complications associated with CRISPR epigenetic editing.

This is a futuristic thing, Natarajan concluded. The combination of genetics and epigenetics is going to be the future of personalized medicine.

The rest is here:
Can High Blood Sugar Haunt People with Diabetes Even After it is Under Control? - BioSpace

Visit the News Hub

Gene in fruit flies, worms, zebrafish, mice and people may help explain some fertility issues

Researchers at Washington University School of Medicine in St. Louis have identified a gene that plays an important role in fertility across multiple species. Pictured is a normal fruit fly ovary (left) and a fruit fly ovary with this gene dialed down (right). Male and female animals missing this gene had substantially defective reproductive organs. The study could have implications for understanding human infertility and early menopause.

A new study from Washington University School of Medicine in St. Louis identifies a specific genes previously unknown role in fertility. When the gene is missing in fruit flies, roundworms, zebrafish and mice, the animals are infertile or lose their fertility unusually early but appear otherwise healthy. Analyzing genetic data in people, the researchers found an association between mutations in this gene and early menopause.

The study appears Aug. 28 in the journal Science Advances.

The human gene called nuclear envelope membrane protein 1 (NEMP1) is not widely studied. In animals, mutations in the equivalent gene had been linked to impaired eye development in frogs.

The researchers who made the new discovery were not trying to study fertility at all. Rather, they were using genetic techniques to find genes involved with eye development in the early embryos of fruit flies.

We blocked some gene expression in fruit flies but found that their eyes were fine, said senior author Helen McNeill, PhD, the Larry J. Shapiro and Carol-Ann Uetake-Shapiro Professor and a BJC Investigator at the School of Medicine. So, we started trying to figure out what other problems these animals might have. They appeared healthy, but to our surprise, it turned out they were completely sterile. We found they had substantially defective reproductive organs.

Though it varied a bit by species, males and females both had fertility problems when missing this gene. And in females, the researchers found that the envelope that contains the eggs nucleus the vital compartment that holds half of an organisms chromosomes looked like a floppy balloon.

This gene is expressed throughout the body, but we didnt see this floppy balloon structure in the nuclei of any other cells, said McNeill, also a professor of developmental biology. That was a hint wed stumbled across a gene that has a specific role in fertility. We saw the impact first in flies, but we knew the proteins are shared across species. With a group of wonderful collaborators, we also knocked this gene out in worms, zebrafish and mice. Its so exciting to see that this protein that is present in many cells throughout the body has such a specific role in fertility. Its not a huge leap to suspect it has a role in people as well.

To study this floppy balloon-like nuclear envelope, the researchers used a technique called atomic force microscopy to poke a needle into the cells, first penetrating the outer membrane and then the nucleuss membrane. The amount of force required to penetrate the membranes gives scientists a measure of their stiffness. While the outer membrane was of normal stiffness, the nucleuss membrane was much softer.

Its interesting to ask whether stiffness of the nuclear envelope of the egg is also important for fertility in people, McNeill said. We know there are variants in this gene associated with early menopause. And when we studied this defect in mice, we see that their ovaries have lost the pool of egg cells that theyre born with, which determines fertility over the lifespan. So, this finding provides a potential explanation for why women with mutations in this gene might have early menopause. When you lose your stock of eggs, you go into menopause.

On the left is a normal fruit fly ovary with hundreds of developing eggs. On the right is a fruit fly ovary that is totally missing the NEMP gene. It is poorly developed and no eggs are visible.

McNeill and her colleagues suspect that the nuclear envelope has to find a balance between being pliant enough to allow the chromosomes to align as they should for reproductive purposes but stiff enough to protect them from the ovarys stressful environment. With age, ovaries develop strands of collagen with potential to create mechanical stress not present in embryonic ovaries.

If you have a softer nucleus, maybe it cant handle that environment, McNeill said. This could be the cue that triggers the death of eggs. We dont know yet, but were planning studies to address this question.

Over the course of these studies, McNeill said they found only one other problem with the mice missing this specific gene: They were anemic, meaning they lacked red blood cells.

Normal adult red blood cells lack a nucleus, McNeill said. Theres a stage when the nuclear envelope has to condense and get expelled from the young red blood cell as it develops in the bone marrow. The red blood cells in these mice arent doing this properly and die at this stage. With a floppy nuclear envelope, we think young red blood cells are not surviving in another mechanically stressful situation.

The researchers would like to investigate whether women with fertility problems have mutations in NEMP1. To help establish whether such a link is causal, they have developed human embryonic stem cells that, using CRISPR gene-editing technology, were given specific mutations in NEMP1 listed in genetic databases as associated with infertility.

We can direct these stem cells to become eggs and see what effect these mutations have on the nuclear envelope, McNeill said. Its possible there are perfectly healthy women walking around who lack the NEMP protein. If this proves to cause infertility, at the very least this knowledge could offer an explanation. If it turns out that women who lack NEMP are infertile, more research must be done before we could start asking if there are ways to fix these mutations restore NEMP, for example, or find some other way to support nuclear envelope stiffness.

This work was supported by the Canadian Institutes of Health, research grant numbers 143319, MOP-42462, PJT-148658, 153128, 156081, MOP-102546, MOP-130437, 143301, and 167279. This work also was supported, in part, by the Krembil Foundation; the Canada Research Chair program; the National Institutes of Health (NIH), grant number R01 GM100756; and NSERC Discovery grant; and the Medical Research Council, unit programme MC_UU_12015/2. Financial support also was provided by the Wellcome Senior Research Fellowship, number 095209; Core funding 092076 to the Wellcome Centre for Cell Biology; a Wellcome studentship; the Ontario Research FundsResearch Excellence Program. Proteomics work was performed at the Network Biology Collaborative Centre at the Lunenfeld-Tanenbaum Research Institute, a facility supported by Canada Foundation for Innovation funding, by the Ontarian Government, and by the Genome Canada and Ontario Genomics, grant numbers OGI-097 and OGI-139.

Tsatskis Y, et al. The NEMP family supports metazoan fertility and nuclear envelope stiffness. Science Advances. Aug. 28, 2020.

Washington University School of Medicines 1,500 faculty physicians also are the medical staff of Barnes-Jewish and St. Louis Childrens hospitals. The School of Medicine is a leader in medical research, teaching and patient care, ranking among the top 10 medical schools in the nation by U.S. News & World Report. Through its affiliations with Barnes-Jewish and St. Louis Childrens hospitals, the School of Medicine is linked to BJC HealthCare.

Original post:
Genetic mutations may be linked to infertility, early menopause - Washington University School of Medicine in St. Louis

When Ralph Fisher,a Texas cattle rancher, set eyes on one of the worlds first cloned calves in August 1999, he didnt care what the scientists said: He knew it was his old Brahman bull, Chance, born again. About a year earlier, veterinarians at Texas A&M extracted DNA from one of Chances moles and used the sample to create a genetic double. Chance didnt live to meet his second self, but when the calf was born, Fisher christened him Second Chance, convinced he was the same animal.

Scientists cautioned Fisher that clones are more like twins than carbon copies: The two may act or even look different from one another. But as far as Fisher was concerned, Second Chance was Chance. Not only did they look identical from a certain distance, they behaved the same way as well. They ate with the same odd mannerisms; laid in the same spot in the yard. But in 2003, Second Chance attacked Fisher and tried to gore him with his horns. About 18 months later, the bull tossed Fisher into the air like an inconvenience and rammed him into the fence. Despite 80 stitches and a torn scrotum, Fisher resisted the idea that Second Chance was unlike his tame namesake,telling the radio program This American Life that I forgive him, you know?

In the two decades since Second Chance marked a genetic engineering milestone, cattle have secured a place on the front lines of biotechnology research. Today, scientists around the world are using cutting-edge technologies, fromsubcutaneous biosensorstospecialized food supplements, in an effort to improve safety and efficiency within the$385 billion global cattle meat industry. Beyond boosting profits, their efforts are driven by an imminent climate crisis, in which cattle play a significant role, and growing concern for livestock welfare among consumers.

Gene editing stands out as the most revolutionary of these technologies. Although gene-edited cattle have yet to be granted approval for human consumption, researchers say tools like Crispr-Cas9 could let them improve on conventional breeding practices and create cows that are healthier, meatier, and less detrimental to the environment. Cows are also beinggiven genesfrom the human immune system to create antibodies in the fight against Covid-19. (The genes of non-bovine livestock such as pigs and goats, meanwhile, have been hacked togrow transplantable human organsandproduce cancer drugs in their milk.)

But some experts worry biotech cattle may never make it out of the barn. For one thing, theres the optics issue: Gene editing tends to grab headlines for its role in controversial research and biotech blunders. Crispr-Cas9 is often celebrated for its potential to alter the blueprint of life, but that enormous promise can become a liability in the hands of rogue and unscrupulous researchers, tempting regulatory agencies to toughen restrictions on the technologys use. And its unclear how eager the public will be to buy beef from gene-edited animals. So the question isnt just if the technology will work in developing supercharged cattle, but whether consumers and regulators will support it.

Cattle are catalysts for climate change. Livestockaccount for an estimated 14.5 percent of greenhouse gas emissions from human activities, of which cattle are responsible for about two thirds, according to the United Nations Food and Agriculture Organization (FAO). One simple way to address the issue is to eat less meat. But meat consumption is expected to increasealong with global population and average income. A 2012reportby the FAO projected that meat production will increase by 76 percent by 2050, as beef consumption increases by 1.2 percent annually. And the United States isprojected to set a recordfor beef production in 2021, according to the Department of Agriculture.

For Alison Van Eenennaam, an animal geneticist at the University of California, Davis, part of the answer is creating more efficient cattle that rely on fewer resources. According to Van Eenennaam, the number of dairy cows in the United Statesdecreasedfrom around 25 million in the 1940s to around 9 million in 2007, while milk production has increased by nearly 60 percent. Van Eenennaam credits this boost in productivity to conventional selective breeding.

You dont need to be a rocket scientist or even a mathematician to figure out that the environmental footprint or the greenhouse gases associated with a glass of milk today is about one-third of that associated with a glass of milk in the 1940s, she says. Anything you can do to accelerate the rate of conventional breeding is going to reduce the environmental footprint of a glass of milk or a pound of meat.

Modern gene-editing tools may fuel that acceleration. By making precise cuts to DNA, geneticists insert or remove naturally occurring genes associated with specific traits. Some experts insist that gene editing has the potential to spark a new food revolution.

Jon Oatley, a reproductive biologist at Washington State University, wants to use Crispr-Cas9 to fine tune the genetic code of rugged, disease-resistant, and heat-tolerant bulls that have been bred to thrive on the open range. By disabling a gene called NANOS2, he says he aims to eliminate the capacity for a bull to make his own sperm, turning the recipient into a surrogate for sperm-producing stem cells from more productive prized stock. These surrogate sires, equipped with sperm from prize bulls, would then be released into range herds that are often genetically isolated and difficult to access, and the premium genes would then be transmitted to their offspring.

Furthermore, surrogate sires would enable ranchers to introduce desired traits without having to wrangle their herd into one place for artificial insemination, says Oatley. He envisions the gene-edited bulls serving herds in tropical regions like Brazil, the worldslargestbeef exporter and home to around 200 million of the approximately 1.5 billion head of cattle on Earth.

Brazils herds are dominated by Nelore, a hardy breed that lacks the carcass and meat quality of breeds like Angus but can withstand high heat and humidity. Put an Angus bull on a tropical pasture and hes probably going to last maybe a month before he succumbs to the environment, says Oatley, while a Nelore bull carrying Angus sperm would have no problem with the climate.

The goal, according to Oatley, is to introduce genes from beefier bulls into these less efficient herds, increasing their productivity and decreasing their overall impact on the environment. We have shrinking resources, he says, and need new, innovative strategies for making those limited resources last.

Oatley has demonstrated his technique in mice but faces challenges with livestock. For starters, disabling NANOS2 does not definitively prevent the surrogate bull from producing some of its own sperm. And while Oatley has shown he can transplant sperm-producing cells into surrogate livestock, researchers have not yet published evidence showing that the surrogatesproduceenough quality sperm to support natural fertilization. How many cells will you need to make this bull actually fertile? asks Ina Dobrinski, a reproductive biologist at the University of Calgary who helped pioneer germ cell transplantation in large animals.

But Oatleys greatest challenge may be one shared with others in the bioengineered cattle industry: overcoming regulatory restrictions and societal suspicion. Surrogate sires would be classified as gene-edited animals by the Food and Drug Administration, meaning theyd face a rigorous approval process before their offspring could be sold for human consumption. But Oatley maintains that if his method is successful, the sperm itself would not be gene-edited, nor would the resulting offspring. The only gene-edited specimens would be the surrogate sires, which act like vessels in which the elite sperm travel.

Even so, says Dobrinski, Thats a very detailed difference and Im not sure how that will work with regulatory and consumer acceptance.

In fact, American attitudes towards gene editing have been generally positive when the modification is in the interest of animal welfare. Many dairy farmers prefer hornless cows horns can inflict damage when wielded by 1,500-pound animals so they often burn them off in apainful processusing corrosive chemicals and scalding irons. Ina study published last yearin the journal PLOS One, researchers found that most Americans are willing to consume food products from cows genetically modified to be hornless.

Still, experts say several high-profile gene-editing failures in livestock andhumansin recent years may lead consumers to consider new biotechnologies to be dangerous and unwieldy.

In 2014, a Minnesota startup called Recombinetics, a company with which Van Eenennaams lab has collaborated, created a pair of cross-bred Holstein bulls using the gene-editing tool TALENs, a precursor to Crispr-Cas9, making cuts to the bovine DNA and altering the genes to prevent the bulls from growing horns. Holstein cattle, which almost always carry horned genes, are highly productive dairy cows, so using conventional breeding to introduce hornless genes from less productive breeds can compromise the Holsteins productivity. Gene editing offered a chance to introduce only the genes Recombinetics wanted. Their hope was to use this experiment to prove that milk from the bulls female progeny was nutritionally equivalent to milk from non-edited stock. Such results could inform future efforts to make Holsteins hornless but no less productive.

The experiment seemed to work. In 2015, Buri and Spotigy were born. Over the next few years, the breakthrough received widespread media coverage, and when Buris hornless descendant graced thecover of Wired magazine in April 2019, it did so as the ostensible face of the livestock industrys future.

But early last year, a bioinformatician at the FDA ran a test on Buris genome and discovered an unexpected sliver of genetic code that didnt belong. Traces of bacterial DNA called a plasmid, which Recombinetics used to edit the bulls genome, had stayed behind in the editing process, carrying genes linked to antibiotic resistance in bacteria. After the agency publishedits findings, the media reaction was swift and fierce: FDA finds a surprise in gene-edited cattle: antibiotic-resistant, non-bovine DNA,readone headline. Part cow, part bacterium?readanother.

Recombinetics has since insisted that the leftover plasmid DNA was likely harmless and stressed that this sort of genetic slipup is not uncommon.

Is there any risk with the plasmid? I would say theres none, says Tad Sonstegard, president and CEO of Acceligen, a Recombinetics subsidiary. We eat plasmids all the time, and were filled with microorganisms in our body that have plasmids. In hindsight, Sonstegard says his teams only mistake was not properly screening for the plasmid to begin with.

While the presence of antibiotic-resistant plasmid genes in beef probably does not pose a direct threat to consumers, according to Jennifer Kuzma, a professor of science and technology policy and co-director of the Genetic Engineering and Society Center at North Carolina State University, it does raise the possible risk of introducing antibiotic-resistant genes into the microflora of peoples digestive systems. Although unlikely, organisms in the gut could integrate those genes into their own DNA and, as a result, proliferate antibiotic resistance, making it more difficult to fight off bacterial diseases.

The lesson that I think is learned there is that science is never 100 percent certain, and that when youre doing a risk assessment, having some humility in your technology product is important, because you never know what youre going to discover further down the road, she says. In the case of Recombinetics. I dont think there was any ill intent on the part of the researchers, but sometimes being very optimistic about your technology and enthusiastic about it causes you to have blinders on when it comes to risk assessment.

The FDA eventually clarified its results, insisting that the study was meant only to publicize the presence of the plasmid, not to suggest the bacterial DNA was necessarily dangerous. Nonetheless, the damage was done. As a result of the blunder,a plan was quashedforRecombinetics to raise an experimental herd in Brazil.

Backlash to the FDA study exposed a fundamental disagreement between the agency and livestock biotechnologists. Scientists like Van Eenennaam, who in 2017 received a $500,000 grant from the Department of Agriculture to study Buris progeny, disagree with the FDAs strict regulatory approach to gene-edited animals. Typical GMOs aretransgenic, meaning they have genes from multiple different species, but modern gene-editing techniques allow scientists to stay roughly within the confines of conventional breeding, adding and removing traits that naturally occur within the species.

That said, gene editing is not yet free from errors and sometimes intended changes result in unintended alterations, notes Heather Lombardi, division director of animal bioengineering and cellular therapies at the FDAs Center for Veterinary Medicine. For that reason, the FDA remains cautious.

Theres a lot out there that I think is still unknown in terms of unintended consequences associated with using genome-editing technology, says Lombardi. Were just trying to get an understanding of what the potential impact is, if any, on safety.

Bhanu Telugu, an animal scientist at the University of Maryland and president and chief science officer at the agriculture technology startup RenOVAte Biosciences, worries that biotech companies willmigrate their experimentsto countries with looser regulatory environments. Perhaps more pressingly, he says strict regulation requiring long and expensive approval processes may incentivize these companies to work only on traits that are most profitable, rather than those that may have the greatest benefit for livestock and society, such as animal well-being and the environment.

What company would be willing to spend $20 million on potentially alleviating heat stress at this point? he asks.

On a windywinter afternoon, Raluca Mateescu leaned against a fence post at the University of Floridas Beef Teaching Unit while a Brahman heifer sniffed inquisitively at the air and reached out its tongue in search of unseen food. Since 2017, Mateescu, an animal geneticist at the university, has been part of a team studying heat and humidity tolerance in breeds like Brahman and Brangus (a mix between Brahman and Angus cattle). Her aim is to identify the genetic markers that contribute to a breeds climate resilience, markers that might lead to more precise breeding and gene-editing practices.

In the South, Mateescu says, heat and humidity are a major problem. That poses a stress to the animals because theyre selected for intense production to produce milk or grow fast and produce a lot of muscle and fat.

Like Nelore cattle in South America, Brahman are well-suited for tropical and subtropical climates, but their high tolerance for heat and humidity comes at the cost of lower meat quality than other breeds. Mateescu and her team have examined skin biopsies and found that relatively large sweat glands allow Brahman to better regulate their internal body temperature. With funding from the USDAs National Institute of Food and Agriculture, the researchers now plan to identify specific genetic markers that correlate with tolerance to tropical conditions.

If were selecting for animals that produce more without having a way to cool off, were going to run into trouble, she says.

There are other avenues in biotechnology beyond gene editing that may help reduce the cattle industrys footprint. Although still early in their development,lab-cultured meatsmay someday undermine todays beef producers by offering consumers an affordable alternative to the conventionally grown product, without the animal welfare and environmental concerns that arise from eating beef harvested from a carcass.

Other biotech techniques hope to improve the beef industry without displacing it. In Switzerland, scientists at a startup called Mootral areexperimenting with a garlic-based food supplementdesigned to alter the bovine digestive makeup to reduce the amount of methane they emit. Studies have shown the product to reduce methane emissions by about 20 percent in meat cattle, according to The New York Times.

In order to adhere to the Paris climate agreement, Mootrals owner, Thomas Hafner, believes demand will grow as governments require methane reductions from their livestock producers. We are working from the assumption that down the line every cow will be regulated to be on a methane reducer, he told The New York Times.

Meanwhile, a farm science research institute in New Zealand, AgResearch, hopes to target methane production at its source by eliminating methanogens, the microbes thought to be responsible for producing the greenhouse gas in ruminants. The AgResearch team isattempting to developa vaccine to alter the cattle guts microbial composition, according to the BBC.

Genomic testing may also allow cattle producers to see what genes calves carry before theyre born, according to Mateescu, enabling producers to make smarter breeding decisions and select for the most desirable traits, whether it be heat tolerance, disease resistance, or carcass weight.

Despite all these efforts, questions remain as to whether biotech can ever dramatically reduce the industrys emissions or afford humane treatment to captive animals in resource-intensive operations. To many of the industrys critics, including environmental and animal rights activists, the very nature of the practice of rearing livestock for human consumption erodes the noble goal of sustainable food production. Rather than revamp the industry, these critics suggest alternatives such as meat-free diets to fulfill our need for protein. Indeed,data suggestsmany young consumers are already incorporating plant-based meats into their meals.

Ultimately, though, climate change may be the most pressing issue facing the cattle industry, according to Telugu of the University of Maryland, which received a grant from the Bill and Melinda Gates Foundation to improve productivity and adaptability in African cattle. We cannot breed our way out of this, he says.

Dyllan Furness is a Florida-based science and technology journalist. His work has appeared in Quartz, OneZero, and PBS, among other outlets. Follow him on Twitter @dyllonline

This article was originally published at Undark and has been republished here with permission. Follow Undark on Twitter @undarkmag

See the original post:
CRISPR cows could boost sustainable meat production, but regulations, wary consumers stand in the way - Genetic Literacy Project

CRISPR is a catchy acronym that originally described a naturally occurring gene editing tool, derived from a bacterial defense mechanism against viruses. Its the name on everybodys lips in the intersecting realms of science, medicine, ethics, and politics. From the moment of its discovery, CRISPR-Cas9 looked like a miraculous solution to all of the problems that gene editing efforts have experienced over decades of trial and error. This revolutionary new gene editing technique has opened the doors to both massive scientific progress and ethical controversy. Now more than ever, were seeing that CRISPR still has massive kinks to work out. Can we ever fully understand the social and scientific implications of gene editing, and should we use it in humans before we learn how to properly harness it?

What is gene editing?

The 20th century saw genetic scientists increasingly focus their pursuits on the sub-microscopic. As science delved deeper into the human body in an attempt to uncover the molecular minutiae of life, the possibility of reaching into the cell and manipulating its genetic material began to look more and more real. Even by the 1950s, evidence had been mounting for decades that deoxyribonucleic acid (DNA), an unassuming molecule residing in a central cellular compartment called the nucleus, was the physical genetic material that passed information from parent to child. Finally, in 1953, landmark work by Kings College biochemist Rosalind Franklin allowed Cambridge researchers to reveal the structure of DNA and confirm its role in heredity once and for all.

Starting from a hesitant foundation, molecular genetics exploded in both scope and popularity over subsequent decades. With the secrets of heredity increasingly out in the open, human ambition demanded that we try to bend DNA to our willand now we can. These days, targeted gene editing techniques revolve around artificially-engineered molecular tools known as nucleases, whose earliest use was in 1996not even 50 years after the discovery of DNAs structure. Engineered nucleases are often described as molecular scissors. Fundamentally, they have two main parts: one part that finds and grabs onto the target DNA within a cell, and one part that snips a piece out of that DNA.

How CRISPR works

CRISPR is similar to other directed nucleases, but its much better at its job. The CRISPR part is secondary to the systems gene editing applications; the truly important discovery, which Jennifer Doudna made in 2012, was a protein that she called CRISPR-associated protein 9, or Cas9. This protein is the nuclease tool, the pair of molecular scissors that finds, sticks to, and snips target DNAand its more accurate than anything weve ever seen before.

In bacteria, CRISPR is a section of the genome that acts as an immune memory, storing little snippets of different viruses genetic material as DNA after failed infections, like trophies. When a once-active virus attempts to invade a bacterium, the mobile helper Cas9 copies down the relevant snippet from CRISPR in the form of ribonucleic acid, or RNA. RNA is a molecule thats virtually identical to DNA, except for one extra oxygen atom. Because of this property, the RNA sequence that Cas9 holds can pair exactly, nucleotide by nucleotide, with the viral targets DNA, making it extremely efficient at finding that DNA. With a freshly transcribed RNA guide, the bacterium can deploy Cas9 to findand cut outthe corresponding section of viral genetic material, rendering the attacker harmless.

The existence of CRISPR in bacteria was old news by 2012, but Doudnas discovery of Cas9s function was revolutionary. With a little creativity and ingenuity, such a simple and accurate nuclease can be modified to be much more than just a pair of scissors. Using synthetic RNA guides and certain tweaks, Cas9 can be used to remove specific genes, cause new insertions to genomes, tag DNA sequences with fluorescent probes, and much more.

The possibilities seem endless.What if we could go into the body of a human affected by a hereditary disease and change that persons DNA to cure them? What if we could modify reproductive germ cells in human bodies (which give rise to sperm and eggs), or make targeted genetic edits in the very first cell of an embryo? Nine months of division and multiplication later, that cell would give rise to a human being whose very nature has been deliberately tweakedand their childrens nature, and their childrens. With the accuracy and accessibility of the CRISPR/Cas9 system, these ideas arent hypotheticals. In 2019, CRISPR edits in bone marrow stem cells were successfully used to cure sickle cell anemia in a Mississippi woman. Beta thalassaemia, another genetic disease of the blood, has also been treated this way. In 2018, Chinese scientist He Jiankui even claimed that he had conferred HIV immunity upon twin girls using embryonic editing.

CRISPRs complications

At first glance, CRISPR looks like a miraclebut it isnt perfect. What if some cells were affected by edits, but others werent, creating a strange genetic mosaic in a human body? What if, in trying to modify a specific gene, we accidentally hit a different section of DNA nearby? What if we got the right gene, but it also affected a different part of the body that we didnt know about?

These problems arent hypotheticals either. So-called mosaicism and off-target editing are huge concerns among CRISPR scientists. Mosaicism is of particular concern in embryonic editing. Though CRISPR injections are carried out when an embryo is single-celled, CRISPR doesnt always appear to work until after several rounds of cell divisionand it doesnt work in every cell. If not all the cells in the body are affected by gene editing that is intended to eliminate a genetic disease, the disease could remain in the body. It may be possible to combat mosaicism with faster gene editing (so that cells dont replicate before theyve had a chance to become CRISPR-modified), altering sperm and egg cells before they meet to form an embryo, and developing more precise CRISPR gene editing which is in itself a challenge, thanks to off-target editing.

In nature, a little bit of off-target editing could actually make the CRISPR-Cas9 defense system stronger with the principle of redundancy. Flexibility in the form of imprecision could allow a bacterium to neutralize viruses whose exact genetic sequences have not yet been encountered: viruses related to, but not identical to, previous attackers. In clinical and therapeutic applications, on the other hand, precision is everything. And unfortunately, as time passes, CRISPRs level of precision seems further and further off. Preprints released just this year reveal that the frequency and magnitude of CRISPRs off-target edits in human cells may be worse than we had previously known. Large proportions of cells with massive unwanted DNA deletions, losses of entire chromosomes in experimental embryos, and shuffling of genetic sequences were observed.

Of course, not only do scientists need to avoid off-target edits, but they also need to know when such undesired edits have occurred. Off-target effects can be detected by genome sequencing and computer prediction tools, but theres no perfect way to do it yetthere may still be editing misses that were, well, missing. Off-target edits themselves could be minimized by altering the RNA transcript that Cas9 carries to make it more accurate, altering Cas9 itself, or reducing the actual amount of Cas9 protein released into the cell (though this could also reduce on-target effects). Replacing Cas9 itself with other Cas variants, like smaller and more easily deliverable CasX and CasY proteins, is a promising possibility for more efficient editing, but these candidates still run into many of the same problems as Cas9. More strategies are constantly being discovered, proposed, and explored, but were still nowhere near perfect.

Perhaps most importantly, even barring any purely technical problems, is that humans remain in sheer ignorance of much of the extent and consequences of pleiotropy, a phenomenon where a genes presence or deletion has more than one effect in the human body. Even genes whose function we think we know well might have totally unexpected additional functions. On the other side of the coin, we dont have a comprehensive understanding of how many different genetic contributors there are to any given trait or disease, much less where they lie in the genome. We dont understand the way that thousands of variations across the entire genome contribute to appearance, personality, and health. Assuming that some genes are good and others are bad is morally dangerous, and scientifically reprehensible. In reality, we are not ready for genetic determinism, and may never be.

A great responsibility

Humanity has discovered a great power, but we all know what comes with great power. Questions of which edits are necessary for health (is mild Harlequin syndrome a disease or a cosmetic concern?), whether edits are ethical (should autism and homosexuality be considered curable conditions?), and the possibility of designer babies, among others, are pertinent and require thorough discussion. We also need to realize that making these types of changes isnt our decision until we can get CRISPR right, and understand the genome well enough to target particular phenotypes. Though most scientists are aware of the difficulties of CRISPR and its use is generally tightly regulated, some scientistsand laypeopleare less careful. He Jiankuis apparent miracle HIV cure led to his arrest and imprisonment for unapproved and unethical practice. Its no great surprise that his work likely fell prey to off-target effects and mosaicism; even if he got it right, his intended change could alter cognitive function, and who knows what else?

Non-scientists are getting involved too: in 2018, self-proclaimed biohacker Josiah Zayner publicly injected his own arm with what he claimed was muscle-enhancing CRISPR. Though Zayner is one of the most vocal, hes not the only one of his kind. Quieter biohackers, untrained people without a scientific background or a good understanding of how CRISPR can go wrong, are attempting to edit themselves and even their pets.

Laypeople have an unquestionable place in science: the scientific discipline needs fresh perspectives and creativity that stuffy academics cant offer. CRISPR is still in its infancy, though. Before we know much, much more about its capabilities and consequences, there can be no place for black market gene editing kits, rogue scientists altering human embryonic and germline DNA, or basement geneticists injecting Cas9 into their dogs. Who can say what effects these interventions might have, not just on edited individuals, but on the futures of entire species?

Some say that gene editing is an act of hubris, destined to backfire spectacularly and horrendously. Others believe that its our responsibility to use CRISPR to improve lives. Which of these opinions is true depends on how science walks a narrow tightrope, though Im inclined to agree with the latterand add that our responsibility is not just to master gene editing, but to make clear and public its many faults and failings. The truth, in all its complexity, needs to overcome pop sciences oversimplification and sensationalism. Promising new advances and techniques are on the horizon, but we have a long way to go. Gene editing is no joke; humanity is playing with fire. With an incredibly accurate and accessible nuclease making its way into labs and garages across the world (while its flaws continue to be uncovered year by year), it is more important than ever for the world to understand and discuss the long-reaching consequences and responsible use of gene editing technology. CRISPR is not a miracle, but gene editing may very well be the future of humanityand its on us to keep it under control.

See the original post here:
The Trouble With CRISPR The Strand - Strand

FT819 CAR T-cell Product Candidate Derived from Clonal Master iPSC Line with Novel CD19-specific 1XX CAR Integrated into TRAC Locus

Phase 1 Clinical Study will Evaluate FT819 for Patients with Advanced B-cell Leukemias and Lymphomas

SAN DIEGO, July 09, 2020 (GLOBE NEWSWIRE) -- Fate Therapeutics, Inc. (NASDAQ: FATE), a clinical-stage biopharmaceutical company dedicated to the development of programmed cellular immunotherapies for cancer and immune disorders, announced today that the U.S. Food and Drug Administration (FDA) has cleared the Companys Investigational New Drug (IND) application for FT819, an off-the-shelf allogeneic chimeric antigen receptor (CAR) T-cell therapy targeting CD19+ malignancies. FT819 is the first-ever CAR T-cell therapy derived from a clonal master induced pluripotent stem cell (iPSC) line, and is engineered with several first-of-kind features designed to improve the safety and efficacy of CAR T-cell therapy. The Company plans to initiateclinical investigation of FT819for the treatment of patients with relapsed / refractory B-cell malignancies, including chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia (ALL), and non-Hodgkin lymphoma (NHL).

The clearance of our IND application for FT819 is a ground-breaking milestone in the field of cell-based cancer immunotherapy. Our unique ability to produce CAR T cells from a clonal master engineered iPSC line creates a pathway for more patients to gain timely access to therapies with curative potential, said Scott Wolchko, President and Chief Executive Officer of Fate Therapeutics. Four years ago, we first set out under our partnership with Memorial Sloan Kettering led by Dr. Michel Sadelain to improve on the revolutionary success of patient-derived CAR T-cell therapy and bring an off-the-shelf paradigm to patients, and we are very excited to advance FT819 into clinical development.

FT819 was designed to specifically address several limitations associated with the current generation of patient- and donor-derived CAR T-cell therapies. Under a collaboration with Memorial Sloan Kettering Cancer Center (MSK) led by Michel Sadelain, M.D., Ph.D., Director, Center for Cell Engineering, and Head, Gene Expression and Gene Transfer Laboratory at MSK, the Company incorporated several first-of-kind features into FT819 including:

The multi-center Phase 1 clinical trial of FT819 is designed to determine the maximum tolerated dose of FT819 and assess its safety and clinical activity in up to 297 adult patients across three types of B-cell malignancies (CLL, ALL, and NHL). Each indication will enroll independently and evaluate three dose-escalating treatment regimens: Regimen A as a single dose of FT819; Regimen B as a single dose of FT819 with IL-2 cytokine support; and Regimen C as three fractionated doses of FT819. For each indication and regimen, dose-expansion cohorts of up to 15 patients may be enrolled to further evaluate the clinical activity of FT819.

At the American Association for Cancer Research (AACR) Virtual 2020 Meeting, the Company presented preclinical data demonstrating FT819 is comprised of CD8 T cells with uniform 1XX CAR expression and complete elimination of endogenous TCR expression. Additionally, data from functional assessments showed FT819 has antigen-specific cytolytic activity in vitro against CD19-expressing leukemia and lymphoma cell lines that is comparable to that of healthy donor-derived CAR T cells, and persists and maintains tumor clearance in the bone marrow in an in vivo disseminated xenograft model of lymphoblastic leukemia.

Fate Therapeutics has an exclusive license for all human therapeutic use to U.S. Patent No. 10,370,452 pursuant to its license agreement with MSK1, which patent covers compositions and uses of effector T cells expressing a CAR, where such T cells are derived from a pluripotent stem cell including an iPSC. In addition to the patent rights licensed from MSK, the Company owns an extensive intellectual property portfolio that broadly covers compositions and methods for the genome editing of iPSCs using CRISPR and other nucleases, including the use of CRISPR to insert a CAR in the TRAC locus for endogenous transcriptional control.

1 Fate Therapeutics haslicensedintellectual propertyfrom MSK on which Dr. Sadelain is aninventor.As a result of the licensing arrangement, MSK has financial interests related to Fate Therapeutics.

About Fate Therapeutics iPSC Product PlatformThe Companys proprietary induced pluripotent stem cell (iPSC) product platform enables mass production of off-the-shelf, engineered, homogeneous cell products that can be administered with multiple doses to deliver more effective pharmacologic activity, including in combination with cycles of other cancer treatments. Human iPSCs possess the unique dual properties of unlimited self-renewal and differentiation potential into all cell types of the body. The Companys first-of-kind approach involves engineering human iPSCs in a one-time genetic modification event and selecting a single engineered iPSC for maintenance as a clonal master iPSC line. Analogous to master cell lines used to manufacture biopharmaceutical drug products such as monoclonal antibodies, clonal master iPSC lines are a renewable source for manufacturing cell therapy products which are well-defined and uniform in composition, can be mass produced at significant scale in a cost-effective manner, and can be delivered off-the-shelf for patient treatment. As a result, the Companys platform is uniquely capable of overcoming numerous limitations associated with the production of cell therapies using patient- or donor-sourced cells, which is logistically complex and expensive and is subject to batch-to-batch and cell-to-cell variability that can affect clinical safety and efficacy. Fate Therapeutics iPSC product platform is supported by an intellectual property portfolio of over 300 issued patents and 150 pending patent applications.

About Fate Therapeutics, Inc.Fate Therapeutics is a clinical-stage biopharmaceutical company dedicated to the development of first-in-class cellular immunotherapies for cancer and immune disorders. The Company has established a leadership position in the clinical development and manufacture of universal, off-the-shelf cell products using its proprietary induced pluripotent stem cell (iPSC) product platform. The Companys immuno-oncology product candidates include natural killer (NK) cell and T-cell cancer immunotherapies, which are designed to synergize with well-established cancer therapies, including immune checkpoint inhibitors and monoclonal antibodies, and to target tumor-associated antigens with chimeric antigen receptors (CARs). The Companys immuno-regulatory product candidates include ProTmune, a pharmacologically modulated, donor cell graft that is currently being evaluated in a Phase 2 clinical trial for the prevention of graft-versus-host disease, and a myeloid-derived suppressor cell immunotherapy for promoting immune tolerance in patients with immune disorders. Fate Therapeutics is headquartered in San Diego, CA. For more information, please visit http://www.fatetherapeutics.com.

Forward-Looking StatementsThis release contains "forward-looking statements" within the meaning of the Private Securities Litigation Reform Act of 1995 including statements regarding the advancement of and plans related to the Company's product candidates and clinical studies, the Companys progress, plans and timelines for the clinical investigation of its product candidates, the therapeutic potential of the Companys product candidates including FT819, and the Companys clinical development strategy for FT819. These and any other forward-looking statements in this release are based on management's current expectations of future events and are subject to a number of risks and uncertainties that could cause actual results to differ materially and adversely from those set forth in or implied by such forward-looking statements. These risks and uncertainties include, but are not limited to, the risk of difficulties or delay in the initiation of any planned clinical studies, or in the enrollment or evaluation of subjects in any ongoing or future clinical studies, the risk that the Company may cease or delay preclinical or clinical development of any of its product candidates for a variety of reasons (including requirements that may be imposed by regulatory authorities on the initiation or conduct of clinical trials or to support regulatory approval, difficulties in manufacturing or supplying the Companys product candidates for clinical testing, and any adverse events or other negative results that may be observed during preclinical or clinical development), the risk that results observed in preclinical studies of FT819 may not be replicated in ongoing or future clinical trials or studies, and the risk that FT819 may not produce therapeutic benefits or may cause other unanticipated adverse effects. For a discussion of other risks and uncertainties, and other important factors, any of which could cause the Companys actual results to differ from those contained in the forward-looking statements, see the risks and uncertainties detailed in the Companys periodic filings with the Securities and Exchange Commission, including but not limited to the Companys most recently filed periodic report, and from time to time in the Companys press releases and other investor communications.Fate Therapeutics is providing the information in this release as of this date and does not undertake any obligation to update any forward-looking statements contained in this release as a result of new information, future events or otherwise.

Contact:Christina TartagliaStern Investor Relations, Inc.212.362.1200christina@sternir.com

View original post here:
Fate Therapeutics Announces FDA Clearance of IND Application for First-ever iPSC-derived CAR T-Cell Therapy - GlobeNewswire

Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 2007;131:86172.

CAS PubMed Article Google Scholar

Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006;126:66376.

CAS PubMed Article Google Scholar

Boland MJ, Hazen JL, Nazor KL, Rodriguez AR, Gifford W, Martin G, et al. Adult mice generated from induced pluripotent stem cells. Nature. 2009;461:914.

CAS PubMed Article Google Scholar

Kang L, Wang J, Zhang Y, Kou Z, Gao S. iPS cells can support full-term development of tetraploid blastocyst-complemented embryos. Cell Stem Cell. 2009;5:1358.

CAS PubMed Article Google Scholar

Zhao XY, Li W, Lv Z, Liu L, Tong M, Hai T, et al. iPS cells produce viable mice through tetraploid complementation. Nature. 2009;461:8690.

CAS PubMed Article Google Scholar

Shi Y, Inoue H, Wu JC, Yamanaka S. Induced pluripotent stem cell technology: a decade of progress. Nat Rev Drug Discov. 2017;16:11530.

CAS PubMed Article Google Scholar

Hasegawa K, Pomeroy JE, Pera MF. Current technology for the derivation of pluripotent stem cell lines from human embryos. Cell Stem Cell. 2010;6:52131.

CAS PubMed Article Google Scholar

Taylor CJ, Bolton EM, Bradley JA. Immunological considerations for embryonic and induced pluripotent stem cell banking. Philos Trans R Soc Lond Ser B Biol Sci. 2011;366:231222.

CAS Article Google Scholar

Devolder K. To be, or not to be? Are induced pluripotent stem cells potential babies, and does it matter? EMBO Rep. 2009;10:12857.

CAS PubMed PubMed Central Article Google Scholar

Fadel HE. Developments in stem cell research and therapeutic cloning: Islamic ethical positions, a review. Bioethics. 2012;26:12835.

PubMed Article Google Scholar

Abad M, Mosteiro L, Pantoja C, Canamero M, Rayon T, Ors I, et al. Reprogramming in vivo produces teratomas and iPS cells with totipotency features. Nature. 2013;502:3405.

CAS PubMed Article Google Scholar

Knoepfler PS. Deconstructing stem cell tumorigenicity: a roadmap to safe regenerative medicine. Stem Cells. 2009;27:10506.

CAS PubMed PubMed Central Article Google Scholar

Hentze H, Soong PL, Wang ST, Phillips BW, Putti TC, Dunn NR. Teratoma formation by human embryonic stem cells: evaluation of essential parameters for future safety studies. Stem Cell Res. 2009;2:198210.

PubMed Article Google Scholar

Tan Y, Ooi S, Wang L. Immunogenicity and tumorigenicity of pluripotent stem cells and their derivatives: genetic and epigenetic perspectives. Curr Stem Cell Res Ther. 2014;9:6372.

CAS PubMed PubMed Central Article Google Scholar

Simonson OE, Domogatskaya A, Volchkov P, Rodin S. The safety of human pluripotent stem cells in clinical treatment. Ann Med. 2015;47:37080.

PubMed Article Google Scholar

Ayala FJ. Cloning humans? Biological, ethical, and social considerations. Proc Natl Acad Sci U S A. 2015;112:887986.

CAS PubMed PubMed Central Article Google Scholar

Taylor CJ, Peacock S, Chaudhry AN, Bradley JA, Bolton EM. Generating an iPSC bank for HLA-matched tissue transplantation based on known donor and recipient HLA types. Cell Stem Cell. 2012;11:14752.

CAS PubMed Article Google Scholar

Okita K, Matsumura Y, Sato Y, Okada A, Morizane A, Okamoto S, et al. A more efficient method to generate integration-free human iPS cells. Nat Methods. 2011;8:40912.

CAS PubMed Article Google Scholar

Lowry WE, Richter L, Yachechko R, Pyle AD, Tchieu J, Sridharan R, et al. Generation of human induced pluripotent stem cells from dermal fibroblasts. Proc Natl Acad Sci U S A. 2008;105:28838.

CAS PubMed PubMed Central Article Google Scholar

Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, et al. Induced pluripotent stem cell lines derived from human somatic cells. Science. 2007;318:191720.

CAS PubMed Article Google Scholar

Sayed N, Liu C, Wu JC. Translation of human-induced pluripotent stem cells: from clinical trial in a dish to precision medicine. J Am Coll Cardiol. 2016;67:216176.

PubMed PubMed Central Article Google Scholar

Yamanaka S. Induced pluripotent stem cells: past, present, and future. Cell Stem Cell. 2012;10:67884.

CAS PubMed Article Google Scholar

Trounson A, DeWitt ND. Pluripotent stem cells progressing to the clinic. Nat Rev Mol Cell Biol. 2016;17:194200.

CAS PubMed Article Google Scholar

Eguchi T, Kuboki T. Cellular reprogramming using defined factors and microRNAs. Stem Cells Int. 2016. https://doi.org/10.1155/2016/7530942.

Article CAS Google Scholar

Moradi S, Asgari S, Baharvand H. Concise review: harmonies played by microRNAs in cell fate reprogramming. Stem Cells. 2014;32:315.

CAS PubMed Article Google Scholar

Ichida JK, Blanchard J, Lam K, Son EY, Chung JE, Egli D, et al. A small-molecule inhibitor of TGF- signaling replaces Sox2 in reprogramming by inducing Nanog. Cell Stem Cell. 2009;5:491503.

CAS PubMed PubMed Central Article Google Scholar

Huangfu D, Maehr R, Guo W, Eijkelenboom A, Snitow M, Chen AE, et al. Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat Biotechnol. 2008;26:7957.

CAS PubMed PubMed Central Article Google Scholar

Li Y, Zhang Q, Yin X, Yang W, Du Y, Hou P, et al. Generation of iPSCs from mouse fibroblasts with a single gene, Oct4, and small molecules. Cell Res. 2011;21:196204.

CAS PubMed Article Google Scholar

Hou P, Li Y, Zhang X, Liu C, Guan J, Li H, et al. Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds. Science. 2013;341:6514.

CAS PubMed Article Google Scholar

Moradi S, Sharifi-Zarchi A, Ahmadi A, Mollamohammadi S, Stubenvoll A, Gunther S, et al. Small RNA sequencing reveals Dlk1-Dio3 locus-embedded MicroRNAs as major drivers of ground-state pluripotency. Stem Cell Rep. 2017;9:208196.

CAS Article Google Scholar

Greve TS, Judson RL, Blelloch R. MicroRNA control of mouse and human pluripotent stem cell behavior. Ann Rev Cell Dev Biol. 2013;29:21339.

CAS Article Google Scholar

Moradi S, Braun T, Baharvand H. miR-302b-3p promotes self-renewal properties in leukemia inhibitory factor-withdrawn embryonic stem cells. Cell J. 2018;20:6172.

PubMed Google Scholar

Lee YJ, Ramakrishna S, Chauhan H, Park WS, Hong S-H, Kim K-S. Dissecting microRNA-mediated regulation of stemness, reprogramming, and pluripotency. Cell Regen. 2016;5:2.

Article CAS Google Scholar

Hassani SN, Moradi S, Taleahmad S, Braun T, Baharvand H. Transition of inner cell mass to embryonic stem cells: mechanisms, facts, and hypotheses. Cell Mol Life Sci. 2019;76:87392.

CAS PubMed Article Google Scholar

Zhu S, Li W, Zhou H, Wei W, Ambasudhan R, Lin T, et al. Reprogramming of human primary somatic cells by OCT4 and chemical compounds. Cell Ctem Cell. 2010;7:6515.

CAS Article Google Scholar

Esteban MA, Wang T, Qin B, Yang J, Qin D, Cai J, et al. Vitamin C enhances the generation of mouse and human induced pluripotent stem cells. Cell Ctem Cell. 2010;6:719.

CAS Article Google Scholar

Xie M, Tang S, Li K, Ding S. Pharmacological reprogramming of somatic cells for regenerative medicine. Acc Chem Res. 2017;50:120211.

CAS PubMed Article Google Scholar

Ma X, Kong L, Zhu S. Reprogramming cell fates by small molecules. Protein Cell. 2017;8:32848.

CAS PubMed PubMed Central Article Google Scholar

Yoshioka N, Gros E, Li HR, Kumar S, Deacon DC, Maron C, et al. Efficient generation of human iPSCs by a synthetic self-replicative RNA. Cell Stem Cell. 2013;13:24654.

CAS PubMed Article Google Scholar

Yakubov E, Rechavi G, Rozenblatt S, Givol D. Reprogramming of human fibroblasts to pluripotent stem cells using mRNA of four transcription factors. Biochem Biophys Res Commun. 2010;394:18993.

CAS PubMed Article PubMed Central Google Scholar

Lee AS, Tang C, Rao MS, Weissman IL, Wu JC. Tumorigenicity as a clinical hurdle for pluripotent stem cell therapies. Nat Med. 2013;19:9981004.

CAS PubMed PubMed Central Article Google Scholar

Gore A, Li Z, Fung HL, Young JE, Agarwal S, Antosiewicz-Bourget J, et al. Somatic coding mutations in human induced pluripotent stem cells. Nature. 2011;471:637.

CAS PubMed PubMed Central Article Google Scholar

Mayshar Y, Ben-David U, Lavon N, Biancotti JC, Yakir B, Clark AT, et al. Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell Stem Cell. 2010;7:52131.

CAS PubMed Article PubMed Central Google Scholar

Tompkins JD, Hall C, Chen VC, Li AX, Wu X, Hsu D, et al. Epigenetic stability, adaptability, and reversibility in human embryonic stem cells. Proc Natl Acad Sci U S A. 2012;109:125449.

CAS PubMed PubMed Central Article Google Scholar

Amps K, Andrews PW, Anyfantis G, Armstrong L, Avery S, Baharvand H, et al. Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol. 2011;29:113244.

CAS PubMed Article PubMed Central Google Scholar

Liang G, Zhang Y. Genetic and epigenetic variations in iPSCs: potential causes and implications for application. Cell Stem Cell. 2013;13:14959.

CAS PubMed PubMed Central Article Google Scholar

Steyer B, Bu Q, Cory E, Jiang K, Duong S, Sinha D, et al. Scarless genome editing of human pluripotent stem cells via transient puromycin selection. Stem Cell Rep. 2018;10:64254.

CAS Article Google Scholar

Giacalone JC, Sharma TP, Burnight ER, Fingert JF, Mullins RF, Stone EM, et al. CRISPR-Cas9-based genome editing of human induced pluripotent stem cells. Curr Protoc Stem Cell Biol. 2018;44:5B7.

PubMed PubMed Central Google Scholar

Zhang XH, Tee LY, Wang XG, Huang QS, Yang SH. Off-target effects in CRISPR/Cas9-mediated genome engineering. Mol Ther Nucleic Acids. 2015;4:e264.

CAS PubMed PubMed Central Article Google Scholar

Guidance for human somatic cell therapy and gene therapy. Hum Gene Ther. 2001;12:30314.

Daley GQ, Hyun I, Apperley JF, Barker RA, Benvenisty N, Bredenoord AL, et al. Setting global standards for stem cell research and clinical translation: the 2016 ISSCR guidelines. Stem Cell Rep. 2016;6:78797.

Original post:
Research and therapy with induced pluripotent stem cells ...

Jul 4th 2020

Editors note: Each of these climate-change articles is fiction, but grounded in historical fact and real science. The year, concentration of carbon dioxide and average temperature rise (above pre-industrial average) are shown for each one. The scenarios do not present a unified narrative but are set in different worlds, with a range of climate sensitivities, on different emissions pathways

IN THE LATE 1980s Michael Crichton, a novelist and filmmaker, had a lucrative idea. He picked up on the work of Allan Wilson, a geneticist at the University of California, Berkeley, and let his imagination run riot. Wilson had extracted DNA from an extinct type of zebra called a quagga. The DNA in question was fragmented, and the extinction of the quagga only a century in the past, but that did not matter. Crichton speculated about recovering far older DNA than the quaggas by looking in the guts of bloodsucking insects preserved in amber that had formed millions of years ago, during the age of the dinosaurs. If the insects had been feasting on dinosaurs, he mused, they might have preserved those creatures DNA. And if you have somethings DNA you could, perhaps, recreate it. The result was Jurassic Park.

Sadly, there is no sign of any real DNA having been preserved from that far back in the past. But be a bit less ambitious in your time-travelling, and apply the three decades worth of biotechnological advances that have happened since Jurassic Park was published to the question of how you might go forward from here, and the aspiration of recreating at least some prehistoric creatures no longer seems completely fanciful. It may, moreover, be of practical importance, because one animal the de-extinctionists have in their sights is the woolly mammoth. And some people believe that reintroducing mammoths into the wild would make a change to the ecology of Earths northern reaches sufficiently large as to help curb global warming.

This, then, is the idea behind the Harvard Woolly Mammoth Revival Project, run by George Church. Unlike the long-dead dinosaurs in Jurassic Park, mammoths were present on Earth as recently as 4,000 years ago. That, and the fact that many of the parts of the world in which they lived are still pretty chilly, means quite a lot of mammoth DNA remains reasonably intact in frozen corpses recovered from the tundraenough for palaeogeneticists to have reconstructed the animals genome. And with a genome, as Crichton mused, you can aspire to produce an animal.

Mammoths are a species of elephant. This helps because two (or, according to some taxonomists, three) other species of these animals remain alive today to provide assistance to the mammoth-revivers. Though African elephants (one species, or possibly two) are closer in size to mammoths than their Asian cousins are, genetics show that the Asian variety are mammoths closest living relatives, so it is they that are the focus of Dr Churchs research.

People once fantasised about cloning a mammoth directly, from cells or cell nuclei somehow revived from a fossil specimen. Dr Churchs approach is less ambitious and more realistic. It is to engineer the crucial elements of mammothness into Asian-elephant cells and then use these modified cells to create beasts which have the characteristics of mammoths, even if they are not strictly the real thing.

The technology that may make this possible is CRISPR-Cas9 gene editing, which permits precise changes to be made at particular places in an existing genome. In the case of mammoths the task does not, at first sight, seem too hard. An Asian elephants genome is 99.96% similar to a mammoths. Unfortunately, the 0.04% of difference amounts to about 1.4m places in the genome where the genetic letters of the DNA message differ between the species. Most of these differences are, admittedly, in places where they probably do not matter. But there are 2,020 exceptions which, collectively, change the nature of 1,642 genesabout 6.5% of the total. It is these differences that make mammoths and Asian elephants distinct.

Dr Churchs team are therefore concentrating on mammothising what they perceive to be the most pertinent of these genomic locations. They are tweaking the genes of laboratory-grown Asian-elephant skin cells one at a time, focusing on changes they hope will promote mammoths famed hairiness, their propensity to store layers of fat beneath their skin, their cold-adapted haemoglobin and even the protein molecules in their cell membranes that act as channels for the passage of sodium ions, and which are also adapted to the cold. Whether they also tinker with genes for size is, for now at least, undecided.

The teams hope, once enough mammothness has been engendered into these cells, is that they can then be induced, by what is now a well-established laboratory procedure, to turn from being skin cells into stem cells. A stem cell is one that has the developmental plasticity needed to give rise to all sorts of other cells as it multiplies. In the short term, this approach will let Dr Church and his colleagues grow tissues such as blood, for further study. In the longer term, perhaps using an artificial womb, a stem cell of this sort might be grown into an embryo that can be brought to term. Not quite a true mammoth. But not a bad imitation.

That is all a huge technical challenge. But it is not completely fanciful. And success would usher in the second part of the plan: to liberate groups of newly created mammothoids into the wild, and let them multiply and change the Earth. This is the long-held dream of another group of researchers, led by Sergey Zimov, who runs the Russian Academy of Sciences Northeast Scientific Station, near Cherskii. Not only is it an attractive idea in its own rightfor who could resist the idea of mammoths once again thundering over Siberia?but it might also alter the climate for the better.

Dr Zimovs plan is a grand project of biogeoengineering. Recreated mammoths are the boldest part of his aspiration to revive the grassland-steppe ecosystem that dominated Siberia until the arrival there of human beings, about 30,000 years ago. It had more or less disappeared by about 10,000 years ago, the end of the Pleistocene epoch, to be replaced by the modern tundra, which is dominated by moss and small trees.

This shift in vegetation was, Dr Zimov and his colleagues believe, a result of the extinction or near-extinction at that time of most of the areas large herbivore species. This was almost certainly a consequence of hunting by human beings. Where once there were woolly rhinoceros, musk ox, bison, saiga, yaks, wild horses and mammoths, there now remain only reindeer and elk. The hooves of those vast herds of herbivores were, he believes, the crucial factor stopping the spread of moss at the expense of grass. And the crashing bulk and appetites of the largest speciesmammoths in particularwould have dealt with young trees before they could grow up, as is still the case for elephants in what remains of Africas savannah. The loss of the grassland, climate modelling suggests, propelled an increase in temperature.

One factor driving this change was that forest and moss are darker than grassland. Their spread has therefore increased the amount of sunlight absorbed by the area they are growing in, causing warming.

A second factor was that large animals helped maintain the soil in the perpetually frozen state known as permafrost, by churning up the winter snowfall and thus bringing the soil into contact with the freezing winter air. But without them, the snow instead forms an insulating blanket that allows the soil beneath to warm up. And when permafrost melts, the organic matter in it breaks down, releasing methane and carbon dioxideboth greenhouse gases.

The third pertinent effect is that grass sequesters carbon in the soil in its roots. In Arctic habitats it would do this better than the small, sparse trees now present, and much better than moss, a type of plant that has no roots. Carbon stored this way is thus kept out of the atmosphere where, in the form of carbon dioxide, it would contribute to global warming. When the grass disappeared, the storage capacity did, too.

All these things point to the idea that restoring the Siberian grasslands at the expense of the tundra would be a good thing to do. And Dr Zimov has indeed made a start at doing so, in an area of tundra, covering 160 square kilometres (62 square miles), near his research station. In 1988 he enclosed part of this area and has gradually populated it with reindeer, Yakutian horses, elk, bison, musk ox, yaks, Kalmykian cows and sheep. These coexist with several species of predator, including lynx, wolverines and brown bears. He calls this rewilding project Pleistocene Park, and thinks it would benefit greatly from having a few mammoths, or even mammoth substitutes, in it as well.

Pleistocene Park is an experiment, but it seems to be working. Grasses now dominate large parts of it, carbon storage in the soil is going up and the rate of nutrient turnover is increasing, too. This last point is important because a faster turnover of nutrients means more animals can be supported by a given areaa prerequisite for re-establishing large herds.

Clearly, for Dr Zimovs project to have any effect on the climate it would have to be carried out on a grand scale. The Northeast Siberian coastal tundra, to give the area of habitat in which Pleistocene Park is located its proper name, covers about 850,000 square kilometres, so the park is, at the moment, a mere pinprick. It would also take many decades, even without the complication of introducing as-yet-imaginary mammothoids into the mix.

Expansive though the tundra is, however, whether that effect will be large enough to weigh in the scales of a planet-sized problem is a matter of debate. The models suggest that the global temperature rise brought about by the shift from steppe to tundra was a bit over 0.1C. Reversing this shift would, presumably, push the temperature down by a similar amount. That, as Chris Field of Stanford University, in California, who was one of the modellers, points out, would help stabilise the climate, provided global temperature rises above preindustrial levels can be kept, by other means, below 1.5-2C, the objective agreed in Paris in 2015. But if the rise were much greater than this, he thinks the permafrost would melt anywaymammoths or no.

This article appeared in the The World If section of the print edition under the headline "Doing the tundra quick-steppe"

More here:
What if mammoths are brought back from extinction? - The Economist

On February 67, 2020, the Simons Foundation Autism Research Initiative (SFARI) convened a two-day workshop to explore the possibility of gene therapies for autism spectrum disorder (ASD), a neurodevelopmental condition associated with changes in over 100 genes. Inspired by the recent, stunning successes of gene therapy for the fatal neuromuscular disorder spinal muscular atrophy (SMA)1, and by the accumulation of genes confidently associated with ASD2, SFARI welcomed a diverse collection of researchers to begin to think about whether a similar approach could be taken for ASD. Because gene therapy attempts to fix what is broken at the level of a causative gene, it would offer a more direct and imminent strategy than mitigation of the many and as yet mostly unclear downstream effects of a damaged gene.

The workshop was organized in 20 talks and several discussion panels, which tackled many outstanding issues, including how to choose candidate target genes and predict outcomes; how to optimize vectors for gene delivery; how to decide when to intervene; which animal models to develop; how to find appropriate endpoints for clinical trials and understand the available regulatory pathways. SFARI also raised the question of how its funding might best propel gene therapy efforts amid the emerging, complex ecosystem of academic laboratories, biotech companies, and pharmaceutical industries.

Even the opportunity to have this discussion is very rewarding, said SFARI Investigator Matthew State of the University of California, San Francisco (UCSF), one of the investigators who directed teams of geneticists to analyze the Simons Simplex Collection (SSC).

These efforts have offered up multiple potentially feasible therapeutic targets. Though rare, de novo disruptive mutations in the highest confidence ASD genes often result in severe impairment characterized not only by social difficulties, but also by intellectual disability and seizures. The combination of a single gene mutation of large effect coupled with particularly severe outcomes that include ASD are likely to offer the most immediate targets for gene therapy. For now, this leaves out a large number of individuals with autism for whom genetic causes are not yet known and are likely the result of a combination of many small effect alleles across a large number of genes.

Highlights from talks and discussion panel, chaired by Rick Lifton of Rockefeller University

In the first talk of the workshop, State brought the group up to speed on ASD genomics. The most recent tally from exome-sequencing in simplex cases of ASD highlighted 102 genes in which rare mutations confer individually large risks2. In contrast, the task of identifying common variants carrying very small risks remains quite challenging, with less than a half dozen alleles so far identified with confidence3. The rare, disruptive mutations that result in loss of function of one gene copy are an attractive focus for gene therapy because of the tractability of targeting a single spot in the genome per individual and because, in the vast majority of cases, there remains a single unchanged allele. This points to ways to boost gene and/or protein expression back toward the normal state by leveraging the unaffected copy. But both the limited number of cases known so far combined with the possibility that different mutations to the same gene may have different effects complicate thinking about how to prioritize targets for gene therapy.

State made several points that were continually touched on throughout the workshop. Many ASD genes are highly expressed during midfetal development in the cortex, and additional experiments will need to determine whether and how long a window of opportunity may be present for successful gene therapy postnatally. Given the relatively small number of people with these conditions, new clinical trial designs are needed that dont rely on comparisons between large control and intervention groups (see also Bryan Kings talk below).

Beyond the gene-crippling mutations found in the exome, disruptions to transcription may also dramatically raise risk for autism and may be corrected with a type of gene therapy using ASOs. SFARI Investigator Stephan Sanders of UCSF focused on the role of splicing, the process by which an initial transcript is turned into messenger RNA by removal of introns and joining together of exons. Splicing is disrupted in at least 1.5 percent of individuals with ASD4, and possibly many more, as suggested by transcript irregularities found in postmortem autism brain5. Sanders described Illuminas Splice AI project in which machine-learning helps predict noncoding variants that can alter splicing, including those beyond typical splice sites found near a gene6. As a result of incorporating sequence information around and between splice sites, this computational tool detected more mutations with predicted splice-altering consequences in people with ASD and intellectual disability than in those without the condition.

An ASO designed to bind specific portions of RNA could conceivably correct errors in transcription. ASOs have already been approved for use in other disorders in order to skip exons, retain exons or to degrade mRNA. Unlike other forms of gene therapy, ASOs do not permanently alter the genome, making it a kind of gene therapy lite. This reversibility has both disadvantages (having to re-infuse the ASO every few months) and advantages (multiple opportunities to optimize the dose and target; serious adverse effects are not permanent).

Jonathan Weissman of UCSF discussed the available toolbox for controlling gene expression developed by many different laboratories. To turn genes on or off, he has developed a method to combine CRISPR with an enzymatically inactive (dead) Cas9, which can then be coupled with a transcriptional activator (CRISPRa) or repressor (CRISPRi)7 (Figure 2). In the case of loss-of-function mutations, Weissman outlined strategies to make the remaining good allele work harder: increase transcription via CRISPRa, decrease mRNA turnover, increase translation of a good transcript via modification of upstream open reading frames (uORFs) or increase a proteins stability, possibly through small molecules acting on the ubiquitin system8. That said, the effects on a cell may be complicated. Using Perturb-Seq screens, Weissman described genetic interaction manifolds that show nonlinear mapping between genotype and single cell transcriptional phenotypes9. Additionally, Weissman summarized recent work from his laboratory that has identified large numbers of uORFs that result in polypeptides, some of which affect cellular function.

SFARI Investigator Michael Wigler of Cold Spring Harbor Laboratories echoed the idea of a gene-therapy strategy that increases expression of the remaining good copy of a gene, especially given that in his estimate, 45 percent of simplex cases of autism carried a de novo, likely disrupting variant. He also called attention to the uterine environment, especially the challenge posed by expression of paternally derived antigens in the fetus and the impact of a potential maternal immune response, and the need to understand how it interacts with de novo genetic events.

Highlights from talks and discussion panel, chaired by Arnon Rosenthal of Alector

The discussion turned to finding ways of getting genes into the central nervous system. The AAV is the darling of gene therapy, given that it does not replicate and is not known to cause disease in humans. A version that can cross the blood-brain barrier (AAV9) was used to deliver a gene replacement to children with SMA intravenously; though this effectively delivered the genetic cargo to ailing motor neurons in the spinal cord, it does not work that well at delivering genes throughout the brain.

Ben Deverman of the Stanley Center at the Broad Institute of MIT and Harvard detailed his efforts to optimize AAV for efficient transduction of brain cells through a targeted evolution process: his team engineers millions of variants in the capsid of the virus, then screens them for entry into the nervous system and transduction of neurons and glia. This has yielded versions (called AAV-PHP.B and AAV-PHP.eB) that more efficiently enter the brain10,11. One successfully delivered the MECP2 gene to the brain of a Rett syndrome mouse model, resulting in ameliorated symptoms and an extended lifespan12. Unfortunately, these viruses dont work in human cells or in all mouse strains. A quick mouse genome-wide association study (GWAS) revealed that the Ly6a gene mediates efficient blood-brain barrier crossing of AAV-PHP.B and AAV-PHP.eB13. Now his group has identified Ly6a-independent capsids that may translate better to humans. He also noted that the PHP.B vectors have tissue specificity for brain and liver.

With an estimated 87 percent of autism-associated genes raising risk through haploinsufficiency (having only one functional gene copy out of the two), SFARI Investigator Nadav Ahituv of UCSF made the case for approaches that boost expression of the remaining good copy of a gene through endogenous mechanisms a strategy he called cis-regulation therapy. This method also provides a way to work around the small four kb payload of AAV, which strains to contain cDNA of many autism genes. A recent study by his group used CRISPRa targeted at an enhancer or promoter of SIM1 and promoter of MC4R, both obesity genes, in mice. Using one AAV vector for a dCas9 joined to a transcription activator, and another AAV vector having a guide RNA targeting either a promoter or an enhancer, and a guide RNA targeting a promoter, the researchers injected the vectors together into the hypothalamus, which resulted in increased SIM1 or MC4R transcription and reversed the obesity phenotype brought on by loss of these genes14. Targeting regulatory elements had the added benefit of tissue specificity, and there seemed to be a ceiling effect for SIM1 expression, which suggested an endogenous safeguard against overexpression at work. He is now collaborating with SFARI Investigator Kevin Bender, also at UCSF, to apply this approach to the autism gene SCN2A.

Botond Roska of the Institute of Molecular and Clinical Ophthalmology in Basel, Switzerland pointed out that getting genes to the cells where they are needed is crucial when treating eye diseases. Off-target effects there can induce degeneration of healthy cells. For this reason, Roska and his group have created AAVs that target specific cell types in the retina by developing synthetic promoters that efficiently promote expression of the viruss cargo15. The promoters they designed were educated guesses based on four approaches: likely regulatory elements close to genes expressed with cell-type specificity in the retina, conserved elements close to cell typespecific genes, binding sites for cell typespecific transcription factors and open chromatin close to cell typespecific genes. Screening a library of these in mouse, macaque and human retina revealed some with high cell-type specificity (Figure 3). Importantly, macaque data predicted success in human retina much better than did mouse data. In preliminary experiments, and more relevant to gene therapy for ASD, these cell-specific vectors also had some success in mouse cortex, for example lighting up parvalbumin neurons or an apparently new type of astrocyte.

Roska also described new methods for delivery, in which nanoparticles are coated with AAV, then drawn into the brain using magnets16. This magnetophoresis technique allows a library of experimental AAVs to be tested at the same time in one monkey. Steering nanoparticles with magnets gives more control of vector placement and gene delivery. He argued that these in the future could access even deep structures of the brain.

Highlights from talks and discussion panel, chaired by Steven Hyman of the Broad Institute at MIT and Harvard

Kathy High of Spark Therapeutics reviewed the story of gene therapy for spinal muscular atrophy (SMA) type 1. Though she was not directly involved in that research, she is well aware of the regulatory atmosphere surrounding gene therapy, given that Spark Therapeutics developed the first approved AAV-delivered gene for a form of retinal dystrophy. The SMA story is a useful case study in that an ASO-based therapy (nusinersen, marketed as Spinraza), approved in 2016, set the stage for a gene-replacement therapy, marketed as Zolgensma (onasemnogene abeparvovec). Ultimately, the amount of data supporting Zolgensmas approval was modest: a Phase one dose study of 15 infants1, and an ongoing Phase three trial of 21 infants and safety data from 44 individuals. Yet the approval was helped by the dramatic results and clear endpoints: those receiving a single intravenous infusion of an AAV9 vector containing a replacement gene all remained alive at 20 months of age, whereas only 8 percent survived to that age in the natural history data, which compiles the diseases untreated course. High mentioned that maintaining product quality for gene therapeutics may prove trickier than for typical medications.

The attractive, highly customizable nature of gene therapy might have a regulatory downside in that different vector payloads, even when designed to do the same thing, could invite separate approval processes. Though not knowing how regulatory agencies would view this, High said that their perspectives are bound to evolve as more gene therapy trials are completed.

Getting to ASD-related syndromes, Bender talked about SCN2A, which encodes the sodium channel Nav1.2. SCN2A mutations in humans can be gain of function or loss of function; gain-of-function mutations are associated with early onset epilepsy, and loss-of-function mutations with intellectual disability and ASD. In a mouse model missing one copy of SCN2A, Bender and his group have discovered a role for SCN2A in action potential generation in the first week after birth, and in synaptic function and maturation afterward through regulation of dendritic excitability18 (Figure 4). Using AAV containing CRISPRa constructs developed with the Ahituv lab, the researchers successfully increased SCN2A expression, and recovered synapse function and maturity, even when done several weeks postnatally. Getting the appropriate dosage is critical since gain-of-function mutations are linked to epilepsy. However, Bender reported even when SCN2A expression increased to double normal levels, no hints of hyperexcitability appeared. We might be able to overdrive this channel as much as we want and actually may not have risk of producing an epileptic insult, he said. Next steps are to figure out the developmental windows for intervention, evaluate changes in seizure sensitivity and extend this kind of cis-regulatory approach to other ASD genes.

Angelman syndrome is another condition that attracts interest for gene therapy, in part because neurons already harbor an appropriate replacement gene. Angelman syndrome stems from mutations to the maternally inherited UBE3A gene, which is particularly damaging to neurons because they only express the maternal allele, while the paternal allele is silenced by an antisense transcript. SFARI Investigator Mark Zylka of the University of North Carolina and colleagues showed in 2011 that this paternal allele could be unsilenced with a cancer drug in a mouse model of Angelman syndrome19. Since then, three companies have built ASOs to do the same thing, and these are going into clinical trials. To get a more permanent therapeutic, Zylka has been developing CRISPR/Cas9 systems to reactivate paternal UBE3A, and preliminary experiments show that injecting this construct into the brains of embryonic mice, and then again at birth, results in brain-wide expression of paternal UBE3A and is long-lasting (at least 17 months). Zylka is now making human versions of these constructs. He later noted rare cases of mosaicism for the Angelman syndrome mutation people with 10 percent normal cells in blood have a milder phenotype20, which suggests that even inefficient transduction of a gene vector could help.

Zylka also made a case for prenatal interventions in Angelman syndrome: studies of mouse models indicate that early reinstatement of UBE3A expression in mouse embryos rescues multiple Angelman syndrome-related phenotypes, whereas later postnatal interventions rescue fewer of these21; for humans, a diagnostic, cell-based, noninvasive prenatal test will be available soon22; ultrasound-guided injections into fetal brain of nonhuman primates have been developed23; prenatal surgeries are now standard of care for spinal bifida; and intervening prenatally decreases the risk of an immunogenic response to an AAV vector or its cargo. During the discussion, it was noted that another benefit of acting early was that less AAV would be needed to transduce a much smaller brain; however, a drawback is the lack of data on Angelman syndrome development from birth to one year of age. This natural history would be necessary for understanding whether a prenatal therapy is more effective than treatment of neonates.

SFARI Investigator Guoping Feng of the Massachusetts Institute of Technology has been investigating SHANK3, a high-confidence autism risk gene linked to a severe neurodevelopmental condition called Phelan-McDermid syndrome, which is marked by intellectual disability, speech impairments, as well as ASD. SHANK3 is a scaffold protein important for organizing post-synaptic machinery in neurons. Mouse studies by Feng have shown that SHANK3 re-expression in adult mice that have developed without it can remedy some, but not all, of their phenotypes, including dendritic spine densities, neural function in the striatum and social interaction24. Furthermore, early postnatal re-expression rescued most phenotypes. This makes SHANK3 a potential candidate for gene therapy; however, it is a very large gene 5.2kb as a cDNA that is difficult to fit into a viral vector. To get around this, Fengs group has designed a smaller SHANK3 mini-gene as a substitute for the full-sized version. Preliminary experiments show that AAV delivery of the mini-gene can rescue phenotypes like anxiety, social behavior and corticostriatal synapse function in SHANK3 knockout mice. Feng also discussed his success in editing the genome in marmosets and macaques using CRISPR/Cas9 technology and showed data from a macaque model of SHANK3 dysfunction25. These models may help test gene therapy approaches and identify biomarkers of brain development closely related to the human disorder.

For people with rare conditions brought on by even rarer mutations, individualized gene therapies can provide a pathway for treatment. SFARI Investigator Timothy Yu of Boston Childrens Hospital/Harvard described his N-of-1 study in treating a girl with Batten disease, a recessive disorder in which a child progressively loses vision, speech and motor control while developing seizures. In a little over a year, an ASO that targeted her unusual splice-site mutation in the CLN7 gene was designed, developed and given intrathecally to the girl26. The lift was in negotiating with the FDA and working with private organizations, not just in the science, Yu said. After a year of treatment with the ASO (dubbed milasen after the girl, Mila), there were no serious adverse events; seizure frequency and duration had decreased (Figure 5); and possibly her decline had slowed. Though she remains blind, without intelligible speech and unable to walk on her own, she was still attentive and could respond happily to her familys voices. The highly personalized framework for this drugs approval is completely different from how medications meant for populations are approved, and it opens a regulatory can of worms, Yu said, though he added that the regulators were willing to countenance drug approval for an individuals clinical benefit.

Rett syndrome is a neurodevelopmental condition caused by mutations to the MECP2 gene that has a substantial research base in mouse models. Over 10 years ago, mouse models highlighted the possibility for therapeutics in this condition when Rett-associated phenotypes were rescued by adding back MECP2, even in adulthood27. This reversibility has spurred interest in gene therapy for Rett syndrome, but getting the MECP2 dose right is critical, said Stuart Cobb of the University of Edinburgh and Neurogene: just as too little MECP2 leads to Rett syndrome, too much also results in severe phenotypes. For this reason, it would be nice to package a replacement MECP2 gene with other regulatory elements to control its expression, but this results in constructs that do not fit into viral vectors. To make more room, Cobb and his colleagues have been able to chop away two-thirds of the MECP2, reserving two domains that interact to make a complex on DNA (Figure 6). Mice with this mini-gene are viable and have near normal phenotypes; likewise, injecting this mini-gene into MECP2-deficient mice extended their survival28. Doubling the dose, however, substantially lowered survival. Putting in safety valves to prevent overexpression is going to be quite important, he said. One idea is to add back a construct containing only the last two exons of MECP2, which is where most Rett mutations land. These would then be spliced into native transcripts (called trans-splicing), and thus their expression controlled by endogenous regulatory elements.

Underscoring the double-edged sword of MECP2 dosage, Yingyao Shao from Huda Zoghbis lab at Baylor described an MECP2 duplication syndrome (MDS) in humans, which features hypotonia, intellectual disability, epilepsy and autism. Experiments in an MDS mouse model, which carries one mouse version and one human version of MECP2, recapitulates some of the phenotypes of the human condition and can be rescued by an ASO targeting the human allele29. Shao described work to optimize the ASO for translation into humans, which involved developing a more humanized MDS model that carries two human MECP2 alleles. An acute injection of the ASO was able to knock down MECP2 expression in a dose-dependent manner in these mice, and RNA levels dropped a week after injection, with protein levels falling a week later. MECP2 target genes also normalized their expression level, and one maintained this for at least 16 weeks post-injection. The ASO also rescued behavioral phenotypes of motor coordination and fear conditioning, but not of anxiety; these corrections followed the molecular effects, and these timelines would be important to keep in mind while designing clinical trials. Shao also noted that overtreatment with the ASO resulted in Rett-associated phenotypes, but that this was reversible, which suggests that some fine-tuning of dosing in humans might be possible.

To avoid overtreatment and toxicity of any MDS-directed therapy, Mirjana Maletic-Savatic, also at Baylor, is leaving no stone unturned in a hunt for MDS biomarkers that can predict, in each individual, the safety of a particular dose and regimen. Such biomarkers would also help monitor individuals during treatment, give information about target engagement and identify candidates for a particular treatment. Anything found to be sensitive to expression levels of MECP2 could also be useful for Rett, though she noted that MECP2 levels measured in blood do not track linearly with gene copy number. Thus, because of interindividual variability, her approach is to collect a kitchen sink of data deriving composite biomarkers that accurately reflect the stage and severity of disease in a given case. She and her colleagues are collecting clinical, genetic, neurocircuitry (such as EEG and sleep waves), immunology and molecular data detected in blood, urine and CSF. These measures are also being explored in induced neurons derived from skin samples of people with MDS. She highlighted two interrelated potential biomarkers in the blood of those with this condition; both measures are downstream targets of MECP2 and are responsive to ASO treatment.

Highlights from Early detection and clinical trial issues talks and panel discussion, chaired by Paul Wang of SFARI

Coming up with objective measures of a persons status either their eligibility for a treatment, or whether the treatment has engaged with its target or even whether the treatment is effective is a real necessity in autism-related conditions, which comprise multiple interrelated behaviors. Eye-tracking methodology may provide such a marker, argued SFARI Investigator Ami Klin of Emory University. Focusing on the core social challenges of autism, Klin, Warren Jones and colleagues have been studying children as they view naturalistic social scenes to quantify their social attention patterns. This has revealed how remarkably early in development social visual learning begins and that this process is disrupted in infants later diagnosed with ASD prior to features associated with the condition appearing. By missing social cues, autism in many ways creates itself, moment by moment, Klin said. In considering gene therapy, it may be useful to know that eye looking (how much a subject looks at a persons eyes, an index of social visual engagement) in particular and social visual engagement in general are under genetic control30; that eye-tracking differences emerge as early as 26 months of age; and that homologies in social visual engagement exist between human babies and nonhuman infant primates.

In getting to a point to test gene therapies, identifying those who need them is essential. Wendy Chung of Columbia University and the Simons Foundation illustrated how diagnosis is yoked closely to therapy. To illustrate this, she described her pilot study of newborn blood spots to screen for SMA; at the start, no treatment was available, but the screen identified newborns for a clinical trial of nusinersin. Notably, the screen only cost an additional 11 cents per baby. In the three years since her pilot screen began, the FDA approved two gene therapies for SMA and the SMA screen was adopted for nationwide newborn screening. Currently she is piloting a screen for Duchenne muscular dystrophy and plans to develop a platform that will allow researchers to add other conditions. In prioritizing genetic conditions for gene therapy, she outlined some ideas for focus, such as genes resulting in phenotypes that would not be identified early without screening, those that are relatively frequent, those that are lethal or neurodegenerative, those with a treatment in clinical trials or with FDA-approved medications, and those conditions that are reversible.

In the meantime, Chung also outlined SFARIs involvement in establishing well-characterized cohorts of individuals with autism, which can help lay a groundwork for gene therapy. People with an ASD diagnosis can join SPARK (Simons Foundation Powering Autism Research for Knowledge), which collects medical, behavioral and genetic information (through analysis of DNA from saliva, at no cost to the participant). If a de novo genetic variant is found in one of ~150 genes, that person is referred to Simons Searchlight, which fosters rare conditions communities and which is also compiling natural history data on people with these mutations.

Bryan King of UCSF discussed how current trial designs for ASD were inadequate for gene therapy trials. As ASD prevalence has grown, parallel design trials with one group receiving an experimental medicine and the other a placebo are the standard, but these wont be possible for the rare conditions that are candidates for gene therapy. Also, change is hard to capture, given the malleable nature of ASD: with no intervention, diagnosis can shift between ASD and pervasive developmental disorder-not otherwise specified (PDD-NOS) in 1284 months (as defined by the DSM-IV). Current scales are subjective and may miss specific items of clinical significance. (Last year, SFARI funded four efforts to develop more sensitive outcome measures.) King outlined other pitfalls in ASD clinical trials, including significant placebo responses, inadequate sample sizes and not being specific enough when asking about adverse effects. King also mentioned improvements that may arise from just enrolling in a study, which could prompt previously housebound families to venture out with their child, which could kick off a cascade of positive effects. He reiterated how, for gene therapy, a natural history comparison group may be more appropriate, combined with solid outcome measures.

SFARI Investigator James McPartland of Yale University then underlined the need for objective biomarkers for clinical trials, for which there are currently none that are FDA qualified for ASD. As the director of the Autism Biomarkers Consortium for Clinical Trials (ABC-CT), he works with other scientists to develop reliable biomarkers that can be scaled for use in large samples across different sites. McPartland noted a biomarker studied in the ABC-CT: an event-related potential (N170) to human faces, which is on average slower in ASD than in typically developing children. He is working on ways to make it easier for people with ASD and intellectual disabilities to participate in biomarker studies and to make them more socially naturalistic. In discussion, he mentioned he thought it would be possible to look for these kinds of biomarkers in younger children.

SFARI Investigator Shafali Jeste of the University of California, Los Angeles recounted her experience in working with children with genetic syndromes associated with neurodevelopmental conditions. Though she is asked to participate in clinical trials for these conditions, she senses the field has some work to do to be ready for these trials, particularly in those with additional challenges such as epilepsy and intellectual disability. Meaningful and measurable clinical endpoints are still insufficient, and there needs to be more ways to improve accessibility of these trials for these rare conditions. This means developing new measures, such as gait-mat technology that senses walking coordination, or EEG measures in waking and sleep, which have been applied to people with chromosome 15q11.2-13.1 duplication (dup15q) syndrome, who have severe intellectual disability and motor impairments. Jeste also emphasized that increasing remote access to some measures can make a big difference for a trial; for example, a trial of a behavioral intervention for tuberous sclerosis complex that required weekly lab visits was disappointingly under-enrolled until researchers revamped it so most of the intervention could be done remotely31.

By grappling with the challenges to gene therapy for ASD, the workshop marked out a faint road map of a way forward. As the scientific questions are answered, the regulatory and clinical trial infrastructure will need to develop apace, and coordination between private, academic and advocacy sectors will be essential. But as gene therapy for diverse human conditions continues to be explored and gene discovery in ASD continues, there is reason to believe that some forms of ASD can eventually benefit from this strategy.This workshop provided a terrific discussion about the challenges in developing targeted gene interventions and their potentially transformative effects as therapies, said John Spiro, Deputy Scientific Director of SFARI. We are grateful to all theparticipants, and SFARI looks forward to translating these discussions into focused funding decisions in the near future.

Back to Top

Continued here:
SFARI | SFARI workshop explores challenges and opportunities of gene therapies for autism spectrum disorder - SFARI News

22 June 2020

CRISPRgenome editing has been successfully used to treat three patients with blood disorders in a clinical trial.

Two US patients with beta-thalassaemia and one with sickle cell disease had their bone marrow stem cells edited to produce a different form of haemoglobin, which is normally only found in fetuses and newborns.

'The results [demonstrate] that CRISPR/Cas9 gene editing has the potential to be a curative therapy for severe genetic diseases like sickle cell and beta-thalassaemia,' said Dr Reshma Kewalrami, CEO and President of Vertex, which is running the study jointly with another US pharmaceutical company, CRISPR Therapeutics.

Both sickle cell and beta-thalassaemia are caused by mutations in a gene that produces haemoglobin, the protein in red blood cells that carries oxygen throughout the body. With limited treatment options, patients are often dependent on blood transfusions.

However, the human body is able to make another form of haemoglobin, encoded in a completely separate gene, which is normally only expressed during fetal development and is switched off soon after birth.

In the clinical trial, blood stem cells were removed from the patients and a control gene that turns off the production of fetal haemoglobin was inactivated. Patients were given chemotherapy to remove remaining bone marrow stem cellsbefore they were replaced by the editedcells. The patients were then able to make fetal haemoglobin as adults.

The results of the ongoing trial, presented at the virtual Annual European Hematology Association Congress, reported that two beta-thalassaemia patients were transfusion independent at five and fifteen months after treatment, and the sickle cell patient was free from painful crises at nine months after treatment.

All three patients suffered significant side effects (from which they all recovered), but these were thought to be as a result of the chemotherapy rather than genome editing. Chemotherapy can also have long-term effects including infertility.

It is hoped that this treatment will have long-lasting and durable effects in patients with inherited blood diseases, and early clinical data appear promising. However, patients will need to be followed up throughout their lives to record any changes.

'These highly encouraging early data represent one more step toward delivering on the promise and potential of CRISPR/Cas9 therapies as a new class of potentially transformative medicines to treat serious diseases,' said Dr Samarth Kulkarni, CEO of CRISPR Therapeutics.

See original here:
CRISPR trial shows promising results for sickle cell and thalassaemia - BioNews