Tag Archives: Crispr-Cas9 system

How to Prepare for Deadly Flu and Nuclear Fallout

Breakthroughs in the science of programmable gene expression inspired DARPA to establish the PReemptive Expression of Protective Alleles and Response Elements (PREPARE) program with the goal of delivering powerful new defenses against public health and national security threats. DARPA has now selected five teams to develop a range of new medical interventions that temporarily and reversibly modulate the expression of protective genes to guard against acute threats from influenza and ionizing radiation, which could be encountered naturally, occupationally, or through a national security event.

The program builds from the understanding that the human body has innate defenses against many types of health threats, but that the body does not always activate these defenses quickly or robustly enough to block the worst damage. To augment existing physiological responses, PREPARE technologies would provide a programmable capability to up- or down-regulate gene expression on demand, providing timely, scalable defenses that are proportional to anticipated threats. Service members and first responders could administer these interventions prior to threat exposure or therapeutically after exposure to mitigate the risk of harm or death.

Influenza: “Researchers working within the PREPARE program seek to improve rates of survival and recovery in catastrophic scenarios for which reliable and scalable countermeasures don’t currently exist,” said Dr. Renee Wegrzyn, the PREPARE program manager….Three PREPARE teams are pursuing multi-pronged approaches to influenza defense and treatment that use programmable gene modulators to boost the human body’s natural defenses against influenza and also weaken the virus’ ability to cause harm by directly neutralizing the viral genomes. If successful, their approaches would potentially protect against virtually all influenza strains — regardless of whether a virus is newly emergent or has developed drug resistance — and would provide near instantaneous immunity, in contrast to traditional vaccines. Additionally, the teams are designing their countermeasures so that they are simple to deliver — for example, as intranasal sprays — reducing the logistical challenge of protecting large numbers of people.A team led by DNARx LLC, under principal investigator Dr. Robert Debs, aims to develop a new DNA-encoded gene therapy that helps patients fight influenza by boosting the natural immune response and other protective functions of their nasal passages and lungs.

Radiation Hazard Symbol

Ionizing Gamma Radiation: Other PREPARE teams are pursuing treatments to protect the body from the effects of ionizing gamma radiation. In humans, radiation poisoning primarily affects stem cells in the blood and gut, yet existing treatments only help to regenerate blood cells, and only with limited effect. There is no possibility for prophylactic administration of these drugs, and most must be delivered immediately following radiation exposure to provide any benefit. There are no existing medical countermeasures for radiation damage to the gut
A team led by the University of California, San Francisco, under principal investigator Dr. Jonathan Weissman, also aims to develop gene therapies to enhance resilience against ionizing radiation. The team’s approach should result in an intravenous or orally available treatment that activates innate defenses in gut and blood stem cells for a period of several weeks.

A Dose of Inner Strength to Survive and Recover from Potentially Lethal Health Threats
New tools for programmable modulation of gene expression could yield enhanced resilience against influenza and ionizing radiation for service members and first responders, DARPA Press Release, June 27, 2019

Assisted Evolution: Engineering Coral Reefs

Imagine ecologists cultivating whole new breeds of trees to restock a devastated wilderness…. Coral conservation has traditionally focused on minimizing damage from insults such as water pollution, invasive starfish, and destructive fishing or tourism. In the Caribbean, some conservationists have worked to “replant” damaged coral. But Gates and Van Oppen [two scientists]  have something more intrusive in mind. They want to try to alter the genetics of coral or the microbes that live on it. They dubb the effort “assisted evolution.”

Coral’s most remarkable characteristic—being an animal that is part plant—is also its Achilles’ heel in a hotter world. Normally, coral polyps—the individual coral organisms, which resemble a sea anemone the size of a pinhead—live in harmony with their algal partners, which help feed the polyps and give corals their bright colors. But during heat waves, the relationship sours. Overheated polyps perceive the algae as an irritant and eject them like unwanted squatters. The coral is left bleached, bone-white and starving. If the heat persists, the coral won’t take in new algae and can die.  The bond between coral and algae is complicated, however, and still not fully understood. Just 25 years ago, for example, researchers believed that coral housed just one variety of symbiotic algae. Now, they have identified hundreds. And they are just beginning to examine the role played by the coral’s microbiome, the menagerie of bacteria that inhabit a coral polyp.

Coral bleaching right.

But the complexity also offers multiple paths for scientists trying to forge a less fragile bond between coral and algae. Today, four major lines of research exist: One involves cross-breeding corals to create heat-tolerant varieties, either by mixing strains within a species or by crossing two species that would not normally interbreed. The second enlists genetic engineering techniques to tweak coral or algae. A third tries to rapidly evolve hardier strains of coral and algae by rearing them for generations in overheated lab conditions. A fourth approach, the newest, seeks to manipulate the coral’s microbiome…

In 2018, Cleves [scientist] became the first to report successfully using the CRISPR-Cas9 gene-editing tool on coral. CRISPR is often touted as a method for making genetically modified species. But Cleves says he isn’t interested in creating new kinds of coral. Rather, he sees CRISPR as a tool for deciphering the inner workings of coral DNA by knocking out, or disabling, genes one by one. He hopes to identify genes that might serve as “master switches” controlling how coral copes with heat and stress—knowledge that could help researchers quickly identify corals in the wild or in the laboratory that are already adapted to heat.

Either way, such efforts to re-engineer coral reefs make people such as David Wachenfeld, chief scientist for the Great Barrier Reef Marine Park Authority here, uneasy. The authority is supposed to protect the reef and regulate activities there. In the past, that meant a hands-off approach. Now, he concedes that “it is almost inconceivable that we’re not going to need these tools.” But, he adds, “That doesn’t mean I’m happy about any of this. This is crisis management.”

He ticks off a list of potential difficulties. Scientists focused on breeding heat-loving coral have to avoid weakening other key traits, such as coping with cold. Introducing a new coral on the scale needed to make a dent on a network of 2900 reefs spanning an area half the size of Texas is a daunting challenge. Even in its damaged state, the Great Barrier Reef still contains hundreds of millions of corals—enough to swamp the genetic impact of new coral species…

Could some kind of “super coral,” as some researchers have dubbed them, also run amok in delicate coral ecosystems.

Excerpts from  The Reef Builders, Science, Mar. 22, 2019

Meddling with Nature: Is it Right? Is it Fair?

Many envisioned environmental applications of newly developed gene-editing techniques such as CRISPR might provide profound benefits for ecosystems and society. But depending on the type and scale of the edit, gene-edited organisms intentionally released into the environment could also deliver off-target mutations, evolutionary resistance, ecological disturbance, and extinctions. Hence, there are ongoing conversations about the responsible application of CRISPR, especially relative to the limitations of current global governance structures to safeguard its use,   Largely missing from these conversations is attention to local communities in decision-making. Most policy discussions are instead occurring at the national or international level even though local communities will be the first to feel the context-dependent impacts of any release. ..

CRISPR gene editing and other related genetic technologies are groundbreaking in their ability to precisely and inexpensively alter the genome of any species. CRISPR-based gene drives hold particular import because they are designed to rapidly spread genetic changes—including detrimental traits such as infertility—through populations of sexually reproducing organisms, to potentially reach every member of a species. Villages in Burkina Faso are weighing the release of gene drive–bearing mosquitoes that could suppress malaria. Nantucket Island residents in the United States are considering the release of genetically engineered white-footed mice to deplete Lyme disease reservoirs. New Zealand communities are discussing the possibility of using genetic methods to eliminate exotic predators.

But what if a gene drive designed to suppress an invasive species escaped its release site and spread to a native population? Or if a coral species gene edited to better adapt to environmental stressors dominated reef ecosystems at the expense of a diversity of naturally evolving coral species and the fish that depend on them ? The gravity of these potential outcomes begs the question: Should humans even be meddling with the DNA of wild organisms? The absence of generally agreed on answers can be used to support calls for moratoria on developing and releasing genetically altered organisms, especially those with gene drives (6).

However, the promising benefits of environmental gene editing cannot be dismissed. Gene drives may provide a long-sought-after tool to control vectors of infectious disease and save millions of human lives. Projects to conserve ecosystems or promote species resilience are often intended to repair human-inflicted environmental damage. Put simply, either using this technology irresponsibly or not using it at all could prove damaging to humans, our welfare, and our planet.

At the international level, the Convention on Biological Diversity (CBD) has enlisted an expert technical panel to, in part, update its Cartagena Protocol (of which the United States is not a party) that oversees transboundary transport of living modified organisms to accommodate gene drive–bearing organisms. The International Union for the Conservation of Nature (IUCN) is also developing policy to address the release of gene-edited organisms. Although the CBD and the IUCN offer fora to engage diverse public feedback, a role largely fulfilled by civil society groups, none of these agencies currently use the broad and open deliberative process we advocate….

Different societal views about the human relationship to nature will therefore shape decision-making. Local community knowledge and perspectives must therefore be engaged to address these context-dependent, value-based considerations.  A special emphasis on local communities is also a matter of justice because the first and most closely affected individuals deserve a strong voice in the decision-making process…Compounding this challenge is that these decisions cannot be made in isolation. Organisms released into local environments may cross regional and even international borders. Hence, respect for and consideration of local knowledge and value systems are necessary, but insufficient, to anticipate the potentially ramifying global implications of environmental release of gene-edited organisms. What is needed is an approach that places great weight on local perspectives within a larger global vision…

The needs of ecosystems could also be given voice to inform deliberative outcomes through custodial human proxies. Inspired by legislative precedent set by New Zealand, in which the Whanganui River was granted legal “personhood,” human representatives, nominated by both an international body like the IUCN and the local community, would be responsible for upholding the health and interests of the ecosystems in question. Proposed gene-editing strategies would be placed in the larger context of alternative approaches to address the public health or environmental issue in question…d

An online registry for all projects intending to release genetically engineered organisms into the environment must be created. Currently, no central database exists for environmental gene-editing applications or for decision-making outcomes associated with their deployment, and this potentially puts the global community at risk…A global coordination task force would be charged with coordinating multiple communities, nations, and regions to ensure successful deliberative outcomes. As a hypothetical example, genetic strategies to eliminate invasive possums from New Zealand must include representatives from Australia, the country likely to be affected should animals be transported outside the intended range. Similarly, the African Union is currently deliberating appropriate governance of gene drive–bearing mosquitoes to combat malaria on a regional scale. 

Excerpts from Natalie Kofl et al.,  Editing nature: Local roots of global governance, Science Magazine, Nov. 2, 2018

De-Extinction: Bring Back the Passenger Pigeon

The Crispr-Cas9 system consists of two main parts: an RNA guide, which scientists program to target specific locations on a genome, and the Cas9 protein, which acts as molecular scissors. The cuts trigger repairs, allowing scientists to edit DNA in the process. Think of Crispr as a cut-and-paste tool that can add or delete genetic information. Crispr can also edit the DNA of sperm, eggs and embryos—implementing changes that will be passed down to future generations. Proponents say it offers unprecedented power to direct the evolution of species.

The technology is widely used in animals. Crispr has produced disease-resistant chickens and hornless dairy cattle. Scientists around the world routinely edit the genes in mice for research, adding mutations for human diseases such as autism and Alzheimer’s in a search of possible cures. Crispr-edited pigs contain kidneys that scientists hope to test as transplants in humans.  Crispr has been discussed as a de-extinction tool since its earliest days. In March 2013 the conservation group Revive & Restore co-organized the first TedXDeExtinction conference in Washington, D.C. Revive & Restore was co-founded by Stewart Brand, the creator of the counterculture Whole Earth Catalog and a vocal advocate for a passenger pigeon revival.

The last known passenger pigeon—a bird named Martha—died in captivity at a Cincinnati zoo in 1914….The first step was to sequence the passenger pigeon genome…Sequencing an extinct species’ genome is no easy task. When an organism dies, the DNA in its cells begins to degrade, leaving scientists with what Shapiro describes as “a soup of trillions of tiny fragments” that require reassembly. For the passenger pigeon project, Shapiro and her team took tissue samples from the toe pads of stuffed birds in museum collections. DNA in the dead tissue left them with tantalizing clues but an incomplete picture. To fill in the gaps, they sequenced the genome of the band-tailed pigeon, the passenger pigeon’s closest living relative.

By comparing the genomes of the two birds, researchers began to understand which traits distinguished the passenger pigeon. In a paper published last year in “Science,” they reported finding 32 genes that made the species unique. Some of these allowed the birds to withstand stress and disease, essential traits for a species that lived in large flocks. They found no genes that might have led to extinction. “Passenger pigeons went extinct because people hunted them to death,” Shapiro says

.Revived passenger pigeons could also face re-extinction. The species thrived in the years before European settlement of North America, when vast forests supported billions of birds. Those forests have since been replaced by cities and farmland. “The habitat the passenger pigeons need to survive is also extinct,” Shapiro says.  But what does it mean to bring an extinct species back? Andre E.R. Soares, a scientist who helped sequence the passenger pigeon genome, says most people will accept a lookalike as proof of de-extinction. “If it looks like a passenger pigeon and flies like a passenger pigeon, if it has the same shape and color, they will consider it a passenger pigeon,” Soares says.

Shapiro says that’s not enough. Eventually, she says, gene-editing tools may be able to create a genetic copy of an extinct species, “but that doesn’t mean you are going to end up with an animal that behaves like a passenger pigeon or a woolly mammoth.” We can understand the nature of an extinct species through its genome, but nurture is another matter. 

After he determines how passenger pigeon DNA manifests in the rock pigeons, Novak hopes to edit the band-tailed pigeon, the passenger pigeon’s closest living relative, with as many of the extinct bird’s defining traits as possible. Eventually, he says, he’ll have a hybrid creature that looks and acts like a passenger pigeon (albeit with no parental training) but still contains band-tailed pigeon DNA. These new-old birds will need a name, which their human creator has already chosen: Patagioenas neoectopistes, or “new wandering pigeon of America.”

Excerpts from Amy Dockser Marcus, Meet the Scientists Bringing Extinct Species Back From the Dead, WSJ, the Future of Everything, Oct. 11, 2018