Tag Archives: CRISPR

A lab experiment shows that we could engineer malaria-carrying mosquitoes to kill themselves off

A new paper showcases how genetic engineering can be used to cause populations of malaria-spreading mosquitoes to self-destroy.

Image credits Egor Kamelev.

An international research effort has shown, in the context of a lab experiment, that male mosquitoes engineered to carry a certain strand of DNA can rapidly destroy entire groups of these blood-sucking insects. The main importance of this experiment is that it showcases that gene-drive technology can be used even in harsh environmental conditions, such as those in sub-Saharan Africa.

This “gene drive” sequence is essentially a damaging mutation that could prove to be a powerful tool against the carriers of malaria.

Drastic measures

“Our study is the first [that] could show that gene-drive technology works under ecologically challenging conditions,” says Ruth Muller, an entomologist who led the research at PoloGGB, a high-security lab in Terni, Italy. “This is the big breakthrough that we made with our study.”

While this experiment has been a success, that doesn’t mean it’s going to be used any time soon. For that to happen, the authors first need to prove that their edited mosquitoes can work in practice — i.e. that they’re safe to release into the wild. Not only that but local governments and residents will have to give their approval before any of the mosquitoes can be released.

Still, with that being said, malaria remains one of the most concerning diseases on Earth. It infects an estimated 200 million people every year, with an estimated annual death toll of around 400,000. This is despite decades of coordinated effort to contain it.

So the authors decided to use the CRISPR gene-editing technique to make mosquitoes, the carriers of the malaria parasite, to self-destroy. They worked with the Anopheles gambiae species, which is native to sub-Saharan Africa. The gene they modified is known as “doublesex”, and is normally carried by healthy females. The modified variant, however, deforms their mouths and reproductive organs, meaning they can’t bite (and thus spread the parasite) nor lay eggs. This is combined with a gene drive, “effectively a selfish type of genetic element that spreads itself in the mosquito population,” says Tony Nolan of the Liverpool School of Tropical Medicine, who helped develop and test the mosquitoes.

Due to the risks involved in releasing these insects into real ecosystems, the experiments were carried out in small cages in a high-security basement lab in London. The modified mosquitoes showed that they can destroy populations of the unmodified insects here.

In order to test them under more natural conditions, however, the team also built a special high-security lab in Italy, specifically designed to keep the mosquitoes in. Here, dozens of gene-edited mosquitoes were released into very large cages containing hundreds of natural mosquitoes. Temperature, humidity, and the timing of sunrise and sunset mimicked the environment in sub-Saharan Africa. In less than a year, the authors report, the population of un-altered mosquitoes was all but wiped out.

Both of these steps were carried out far from the insects’ natural range as extra insurance in case any of them got out.

Whether such an approach will ever actually be used in real-life settings is still a matter of much debate. Even so, the study showcases one possible approach and strongly suggests that it would also function in the wild. It’s also a testament to how far gene-editing technology has come, that we could potentially have one of the most threatening (to us) species right now effectively destroy itself.

The paper “Gene-drive suppression of mosquito populations in large cages as a bridge between lab and field” has been published in the journal Nature Communications.

Sugar just got a bit CRISPR: precise gene edits can improve sugarcane resilience, reduce its environmental impact

Ayman Eid, CABBI Postdoctoral Research Associate at the University of Florida, displays gene-edited sugarcane with reduced chlorophyll content. Credit: Rajesh Yarra, UF/IFAS Agronomy.

Sugarcane is one of the most important plants on Earth — at least for us humans. Not only does it provide 80% of the sugar and 30% of the bioethanol consumed worldwide, but the oil in its leaves and stems is also used to make bioplastics.

But there are two big problems with sugarcane. The first is its environmental impact. It takes huge amounts of water to grow and refine sugar (around nine gallons for a single teaspoon), and the whole process produces a lot of waste. To make matters even worse, sugar takes up large portions of agricultural land, fueling deforestation in several parts of the world.

For researchers, this environmental impact is also an opportunity — an opportunity to change the plant and make it more sustainable. But there’s another, different problem with sugar: it has a complex and messy genome, which makes it very difficult to change and edit it. It often takes over a decade for a single sugarcane cultivar to be properly developed, and crossbreeding sugarcane is notoriously difficult.

But new genetic tools can finally enable researchers to edit sugarcane in desired ways, says Fredy Altpeter, Professor of Agronomy at the University of Florida’s Institute of Food and Agricultural Sciences

“Now we have very effective tools to modify sugarcane into a crop with higher productivity or improved sustainability,” Altpeter said. “It’s important since sugarcane is the ideal crop to fuel the emerging bioeconomy.”

Altpeter and Postdoctoral Research Associate Ayman Eid used the so-called “genetic scissors” CRISPR. CRISPR is a family of DNA sequences found in the genomes of some bacteria and archaea and can be used to edit parts of the genome of both plants and animals, eliminating some sequences and replacing them with more desirable ones. This approach can be used to treat diseases in humans or animals, but also for improving crops.

In two studies, the two researchers and their colleagues did just that: edited the gene of sugarcane using the CRISPR. In the first study, they changed a few genes to change the appearance of the plant. This was more of a proof of concept, to know if it worked or not. They also turned off several copies of a gene that helps sugarcane produce chlorophyll, making the plants turn light green or even yellow. The light green ones seemed to require less fertilizers to grow while producing the same biomass and no detectable side effects, the researchers note.

In the second study, researchers replaced individual nucleotides (the individual building blocks of both RNA and DNA) with better versions that they hoped would give sugarcane more resistance to herbicides. Essentially, this meant editing the plant’s own DNA repair process and making it more resilient to herbicides.

The fact that both attempts worked offers great hope for breeding useful new varieties of sugarcane that can help reduce its dreadful environmental impact.

With conventional breeding, two different types of sugarcane would have been cross-bred to reshuffle the genetic information, hoping that the desirable trait (such as needing less fertilizer) is enhanced. The problem is that it’s not always possible to fully control this, and genes are transferred from parents to offspring in blocks, which means that the desired gene is linked to other, superfluous genes. Researchers often have to do multiple rounds of breeding, and screen the plant to see exactly what changed in the offspring. Genetic tools offer a much more elegant, cheaper, and quicker way to accomplish the same thing.

Of course, whether or not consumers will accept CRISPR-edited plants on the plates remains to be seen. Consumers are almost always wary of modifying the genes of plants, even when the scientific process has been shown to be safe.

Journal Reference: Ayman Eid et al, Multiallelic, Targeted Mutagenesis of Magnesium Chelatase With CRISPR/Cas9 Provides a Rapidly Scorable Phenotype in Highly Polyploid Sugarcane, Frontiers in Genome Editing (2021). DOI: 10.3389/fgeed.2021.654996

Mehmet Tufan Oz et al, CRISPR/Cas9-Mediated Multi-Allelic Gene Targeting in Sugarcane Confers Herbicide Tolerance, Frontiers in Genome Editing (2021). DOI: 10.3389/fgeed.2021.673566

How CRISPR could help us discover and treat rare cancers

Bacteria readily acquires a sequence of other species’ DNA into their own, in specific areas that we now call CRISPR. In the lab, CRISPR was synthesized by linking together two guide RNA sequences into a format that would provide the target information and allow us to edit multiple genes simultaneously.

Cancer is a genetic disease, it works by creating certain changes to genes that control the way our cells function, especially how they grow and divide. Some rare cancers, sarcomas in particular, have been treated using CRISPR, which is why the gene-editing tool seems like a good diagnostic and therapeutic tool in the future of cancer treatments.

Obtaining rare cancerous tumors for research is difficult, but luckily organizations such as Pattern.org and the Rare Cancer Research Foundation (RCRF) come into play. These sister groups perform a matching program that enables patients to directly donate their tumor tissue and medical data to research. All the data generated by the project is freely available to the research community and is dedicated to open science.

“Using Pattern.org, the Broad Institute of MIT and Harvard has created over 40 next-generation de-identified cancer models,” Ms. Barbara Van Hare, Director of Foundation partnerships at RCRF said, “These models and associated data will be shared within the worldwide research community.”

After procuring these rare disease samples, Dr. Jesse Boehm from Eli and Edythe L. Broad Institute might have the answer to decipher the genetic landscape of cancer cells and use that to our advantage. Dr. Boehm is the scientific director of the Broad Institute’s Cancer Dependency Map Initiative where he works on the cancer cell line factory project and the cancer dependency map.

Cancer samples are broken apart into cell models and are coaxed into growing in different conditions over a year-long time period. The data from these new cell models are then shared broadly with the world. This is a pipeline activity called the cell line factory. It is a part of an international effort to create a large reference data set, that is called the cancer dependency map.

The cancer dependency map has a two-pronged approach, first by testing cell lines against drugs and then pooled CRISPR screening. First, all cell lines are systematically tested against all drugs developed for any disease. Some known drugs have shown to be effective against certain cancers, clinical trials are swift as these are existing therapies.

“There are 20,000 proteins in the human genome and only 6000 drug therapies. Only five percent of human genes can be targeted with drugs. The cancer dependency Map is completed with the help of CRISPR,” Dr Boehm said.

Pooled CRISPR screening is used and 100,000 CRISPRs target every gene in the genome. Every cell is challenged with all these CRISPRs and at the end of the experiment, the abundance is compared to the beginning of the experiment.

CRISPR is used to snip genes,the DNA repairs creating a broken gene. Cells that are required for viability die and drop out of the population. CRISPRs are bar coded, so if by the end of the experiment the CRISPR is absent, it targets the gene that the cell needed to survive. The genes that drop out are good drug targets, most of these make way for drug discovery projects right away.

“CRISPR is such a sharp tool, it inspires a lot more confidence than its predecessors,” Dr Boehm said. He uses the analogy of Google Maps for this project: “It needs to tell clinicians what to do and where to go, but for it to be relevant-the data needs to be dense enough in that area.”

An additional therapy for cancers involves making four genetic modifications to T cells (immune cells that can kill cancer). It basically adds genes to T cells to fight cancer. One of these is a synthetic gene that gives the T cells a protein that can identify cancer cells better. CRISPR is also used to mute three genes that limit the cells’ cancer-killing abilities (Stadtmauer et al. 2020). With these limiting genes removed, the T cells are less inhibited to fight cancer.

These therapeutics and the Cancer dependency map will take a few decades to develop but will prove to be a very sharp tool in our arsenal against rare cancers when complete.

References:

  • Boehm JS, Golub TR. An ecosystem of cancer cell line factories to support a cancer dependency map. Nat Rev Genet. 2015 Jul;16(7):373-4.
  • M. Jinek, K. Chylinski, I. Fonfara, M.Hauer, J.A. Doudna, E. Charpentier, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337 (2012), pp. 816–821.
  • Stadtmauer, E. A., Fraietta, J. A., Davis, M. M., Cohen, A. D., Weber, K. L., Lancaster, E., … & Tian, L. (2020). CRISPR-engineered T cells in patients with refractory cancer. Science, 367(6481).
  • Tsherniak, A., Vazquez, F., Montgomery, P. G., Weir, B. A., Kryukov, G., Cowley, G. S., … & Meyers, R. M. (2017). Defining a cancer dependency map. Cell, 170(3), 564-576.

Scientists use gene editing on ‘elite males’ for better livestock breeding

Credit: Pixabay.

In order to breed livestock with more desirable traits for food production, such as disease resistance, better meat, and dairy quality, or heat tolerance, many farmers employ selective breeding or more modern techniques such as artificial insemination. Both approaches, however, have their limitations that could be superseded by gene editing with CRISPR technology, scientists argue in a new study.

Although food availability has increased along with the growing human population over the last 30 years, there are still 800 million people suffering from malnutrition, most of whom live in developing nations. In areas where food security is lacking, ruminant livestock (i.e. sheep and goats) often plays a crucial role in the food chain. But while the population of livestock has relatively kept up with our growing nutritional needs, there is still much room for improvement.

For the last six years, an international scientific collaboration involving researchers at Washington State University, Utah State University, University of Maryland, and the Roslin Institute at the University of Edinburgh in the U.K., has been working on speeding up and improving livestock food production using gene-editing techniques.

In a new study, the researchers have presented their findings. They claim they have created pigs, goats, and cattle that can serve as “surrogate sires” — initially sterile males that produce sperm carrying only the genetic traits of an “elite” donor animal. In this context, “elite” refers to animals that have genetic traits that make them more resistant to disease and produce offspring with desirable characteristics in terms of food production.

“With this technology, we can get better dissemination of desirable traits and improve the efficiency of food production. This can have a major impact on addressing food insecurity around the world,” said Jon Oatley, a reproductive biologist with Washington State University’s College of Veterinary Medicine. “If we can tackle this genetically, then that means less water, less feed and fewer antibiotics we have to put into the animals.”

Oatley and colleagues used CRISPR-Cas9 to breed mice, pigs, goats, and cattle that lacked a gene called NANOS2. The gene encodes the expression of molecules that are specifically related to male fertility (i.e. sperm production).

Males lacking the gene grew up sterile but otherwise healthy. They then received a transplant of sperm-producing cells in their testes from other animals. The animals then produced sperm that had the genetic material from the donor.

Surrogate mice fathered healthy offspring who turned out to carry the genes of the donor mice. The researchers also bred sterile male pigs, goats, and cattle, but these larger animals haven’t mated yet.

“This shows the world that this technology is real. It can be used,” said Whitelaw. “We now have to go in and work out how best to use it productively to help feed our growing population.”

Farmers often use artificial insemination to breed livestock such as cattle that have the most desirable genetic characteristics. However, this is an expensive breeding technique that requires either animal proximity or strict control of their movements. For goats, artificial insemination is even more challenging, often requiring surgical procedures.

“Goats are the number one source of protein in a lot of developing countries,” Irina Polejaeva, a professor at Utah State University, said in a statement. “This technology could allow faster dissemination of specific traits in goats, whether it’s disease resistance, greater heat tolerance or better meat quality.”

This is where surrogate sire technology could come in handy, enabling ranchers and herders to have their animals roam freely. Females with a deactivated NANOS2 gene remain fertile, so they can be subsequently used to birth sterile males to be used as surrogate sires.

That being said, this approach is currently impossible at a commercial scale due to regulations, as well as public perception. According to Oatley, gene editing involves making specific, small changes that could occur naturally, and does not combine DNA from different species.

“Even if all science is finished, the speed at which this can be put into action in livestock production anywhere in the world is going to be influenced by societal acceptance and federal policy,” said Oatley. “By working with policymakers and the public, we can help to provide information assuring the public that this science does not carry the risks that other methods do.”

The findings appeared in the Proceedings of the National Academy of Sciences.

CRISPR coronavirus test can diagnose COVID-19 in 40 minutes rather than hours

The CRISPR-Cas12 system for COVID-19 diagnosis. Credit: Mammoth Biosciences.

Lifting the lockdown and moving on with our lives is predicated on massive testing for the coronavirus among the population. There’s really no way around it. An inexpensive new diagnostic test for COVID-19 based on the gene-editing tool CRISPR might prove extremely valuable in this regard. According to researchers at the UC San Francisco and Mammoth Biosciences who devised it, the test could offer a diagnosis in under 40 minutes.

Accurate testing at home by non-experts

The most commonly used COVID-19 test is known as RT-PCR, short for “reverse transcription-polymerase chain reaction”. It’s the same type of test that doctors use to diagnose HIV, measles, and mumps. This kind of test delivers an answer in 4-6 hours and requires expensive lab equipment and highly trained medical staff.

In contrast, the CRISPR test can return a result in well under an hour and can be performed at home, without the need for any special equipment — or the need for specially trained personnel. But how does it work?

CRISPR is a powerful gene-editing tool that allows scientists to dial in on specific bits of DNA inside cells and alter that piece of DNA. Since it was first unveiled in 2012, CRISPR technology has been used extensively to turn genes on and off without having to alter their sequence. But the technology has also proven highly controversial, especially after Chinese scientist He Jiankui used CRISPR on human embryos that ended up being carried to term and born in late 2018.

In this case, CRISPR in conjunction with a protein called Cas-12 and bits of viral genetic material designed to guide it, the researchers designed a test that targets two coronavirus genes (N and E genes).

Coronavirus tests designed by the CDC home in on the N gene while those made by the World Health Organization (WHO) target the E gene to spot COVID-19 cases. The new CRISPR test looks at both genes, allowing for a more robust (and quicker) diagnosis.

How it works

Like the standard PCR tests, the diagnosis first starts with a nasal swab from a patient. The swab is then introduced into the CRISPR-based test that can run multiple samples at once. When the CRISPR-Cas12 system recognizes genetic signatures from the coronavirus, a fluorescent molecule is released signaling the presence of the virus. The change of color determines whether a test is positive or not, similarly to a pregnancy test.

The test was developed in under three weeks and was trialed on a clinical sample of 36 COVID-19 patients and 42 patients with other viral respiratory infections. The results, which were published in the journal Nature Biotechnology, showed that the CRISPR-based DETECTR assay had a 95% positive predictive agreement and a 100% negative predictive agreement.

“The introduction and availability of CRISPR technology will accelerate deployment of the next generation of tests to diagnose COVID-19 infection,” said Charles Chiu, MD, PhD, professor of laboratory medicine at UCSF and co-lead developer of the new test

The process is much faster and less resource-intensive than traditional PCR-based tests. Although it is slightly less sensitive than PCR-based tests, the CRISPR kit can detect as few as 3.2 viral copies of the virus per microliter — a volume many times smaller than a drop of water. Since COVID-19 patients typically have a much higher viral load, the difference shouldn’t have a noticeable impact on diagnosis.

This test was developed in record time and there are many things that can be improved. Chiu and colleagues plan on turning the test into a handheld device with disposable cartridges that can be used by non-experts at home. The test is pending approval by the U.S. Food and Drug Administration (FDA) and once it passes regulatory roadblocks, it could soon enter mass production.

CRISPR gene-editing therapy inserted in the human body for the first time

In a world’s first, scientists have directly administered a CRISPR–Cas9 gene therapy in a patient suffering from a hereditary blindness disorder. The clinical trial, named BRILLIANCE, is still ongoing.

Credit: NIH Image Gallery.

The aim of the trial is to see whether removing a mutation that causes Leber’s congenital amaurosis 10 (LCA10) — the leading cause of childhood blindness in the world for which there is no cure — might reverse the disease.

Researchers at the Oregon Health & Science University in Portland, in collaboration with pharmaceutical companies Editas Medicine (USA) and Allergen (Ireland), encoded the components of the CRISPR gene therapy into a virus that was injected directly into the eye of the patient.

The therapy targets a mutation in the gene CEP290 that is known to cause LCA10.

Previously, clinical trials involving CRISPR-Cas9 edited the genomes of cells that had been removed from the body and later infused them into the patient. In contrast, this time the therapy was inserted directly into the live human body.

For now, there are no details concerning the procedure, such as when it took place or how the patient is fairing. According to the researchers though, it might take a month before the patient should start restoring vision.

However, this isn’t the first time that gene-editing has been used in the human body. Previously, researchers used an older gene-editing technique called zinc-finger nuclease on live patients suffering from Hunter’s syndrome. The results suggest that the procedure was safe; however, there were little signs that the disease’s symptoms improved.

Scientists think that BRILLIANCE is different, betting on CRISPR-Cas9’s superior accuracy and versatility. What’s more, other gene-editing techniques aren’t suited at all for treating LCA10 since they typically require inserting a healthy copy of the mutated gene into the affected cells. The CEP290 gene, however, is much too large to fit into a viral genome. With CRISPR, you don’t have to insert the entire gene — you simply encode instructions that remove the mutation.

Patients suffering from LCA10 still have photoreceptors in their retina that should theoretically allow them to see — it’s just that the mutation disables these cells. Scientists hope that once the therapy advances, these sensing cells will become activated and the patient will be able to see.

“This is one of the few diseases where we think you could actually get an improvement in vision,” Mark Pennesi, a specialist in inherited retinal diseases at Oregon Health & Science University in Portland told Nature.

There shouldn’t be any safety issues since the gene-editing tool stays in the eye and doesn’t travel to other body parts.

Even if the therapy doesn’t work as intended, the trial is a milestone in gene editing, signaling that medicine is ready to make the leap from treating cells in a dish. And if all goes well, researchers plan on testing the therapy on 18 children and adults.

How CRISPR-Cas9 gene editing is set to change the world

CRISPR is a highly precise new method of gene-editing. Image credits: National Human Genome Research Institute

From The Island of Dr. Moreau to Bladerunner to Gattaca, the world of sci-fi on the silver screen has had a long interest in genetic manipulation. Films such as these often portray gene editing as the next big Frankenstein’s monster of biology, which is hardly a positive portrayal. Moreover, it isn’t an accurate one. The world of gene editing is a lot more complex than that.

What’s more, it’s not just sci-fi; gene editing is quickly becoming a reality. It’s too late to put the genie back into the bottle. That’s due in no small part to the fact that gene editing is a lot more accessible today than in decades past. As such, even if some countries decided to pass bans against the practice, others could continue ahead apace, creating an unequal scientific playing field on the subject of genetics.

Today, accessibility and gene editing often mean one tool in particular — CRISPR. Written in full, the tool is called Clustered Regularly Interspaced Short Palindromic Repeats. This almost certainly doesn’t clear up for you what this actually is or does, however, so let’s take a closer look at one of the leading gene editing tools in the toolbox and how it can be put to work to benefit us.

CRISPR 101

For those not in the know, CRISPR is a gene-editing tool that is developed from a natural means by which microbial bacteria edit out pieces of DNA. When a virus infects bacteria, it injects DNA or RNA into the cell, which responds by releasing a form of nuclease (Cas9) to take a snippet of the DNA or RNA sequence and store something equivalent to a genetic memory of the infection. That way, the cell has a memory of and thus a defense against infection from such a virus in the future.

The type of CRISPR we employ works in a similar fashion, snipping out DNA and RNA strands that we wish to use for a given purpose and replacing them with a DNA strand that we would prefer to have in its place. Imagine DNA to be a series of multi-colored Lego bricks. CRISPR-Cas9 thus essentially works by identifying the sequence of colored Legos that we’d want to replace, breaking them off, and replacing them with new bricks.

CRISPR and Gene Therapy

Why do this?

Think of all the diseases that exist due to faulty or damaged DNA. With a technique such as CRISPR gene editing, and the almost infinite choice of Crispr-Cas9 lentivirus vectors, we could in theory snip out the damaged or dangerous DNA strands and replace them with “healthy” sequences.”

Consider horrible and currently incurable diseases such as forms of cancer and Huntington’s disease. We could, in theory, snip out the parts of DNA sequences that code for many horrible conditions, such as sickle cell disease, and replace them with “healthy” substitutes, thereby dramatically improving the condition of or even potentially curing the patient. 

CRISPR for Plants and Animals

There are other benefits that can come from CRISPR as well, not the least of which being work that can be done with animals. Genetic manipulation of animals has already gone on for decades, perhaps millennia if you include the way in which we as human beings have domesticated and bred animals to suit our needs. Modern genetic engineering has taken that focus on animal breeding and “improvement” to a whole new level.

Instead of simply breeding semi-blindly and hoping that we get a good result from animals that display positive genetic traits that we wish to emphasize, we can simply cut into their DNA sequences and insert samples of that species’ DNA that codes for traits we like. The same can be done with plants.

On one hand, that’s certainly a bit close to playing Dr. Frankenstein with nature.

On the other hand, that’s also a potential way to breed more and larger food and this can be a huge game-changer in the fight against world hunger.

That’s because CRISPR is, at the end of the day, a tool with its ultimate nature determined by how we use it. Shelley’s Victor Frankenstein seeks to play God and conquer “life and death,” imagining himself as being by his creations as the “creator and source” of a new species. At its noblest, CRISPR isn’t about playing God with different species but rather helping improve the life of our own.

The world’s first gene-engineered reptiles are all albinos

Researchers report producing the first gene-edited reptiles ever.

An albino lizard hatchling.
Image credits Doug Menke.

A new study reports on the use of CRISPR-Cas9 to create albino brown anole lizards (A. sagrei). No other team has successfully applied gene-editing techniques to reptiles. The study also shows that the gene-edited lizards can also pass the modified genes for albinism to their offspring.

CRISPy lizards

“For quite some time we’ve been wrestling with how to modify reptile genomes and manipulate genes in reptiles, but we’ve been stuck in the mode of how gene editing is being done in the major model systems,” says corresponding author Doug Menke, an associate professor at the University of Georgia.

“We wanted to explore anole lizards to study the evolution of gene regulation, since they’ve experienced a series of speciation events on Caribbean islands, much like Darwin’s finches of the Galapagos.”

In most model species (such as lab rats, for example) CRISPR-Cas9 is employed by injecting gene-editing vectors into freshly fertilized eggs or single-cell zygotes (i.e. after fertilization). However, this approach can’t be used on reptiles, as they employ an internal fertilization process making it hard to predict when an egg becomes fertilized. It’s also hard to isolate a single-celled embryo from momma lizard, which means we can’t transfer it out into a lab dish and work on it.

Menke and his team, however, noticed that the transparent membrane over the species’ ovary allowed them to track all of the developing eggs, including which eggs were going to be ovulated and fertilized next. They then decided to inject the CRISPR elements into unfertilized eggs within the ovaries.

“Because we are injecting unfertilized eggs, we thought that we would only be able to perform gene editing on the alleles inherited from the mother. Paternal DNA isn’t in these unfertilized oocytes,” Menke says.

He explains that it took three months for the lizards to hatch, and says that the procedure is “a bit like slow-motion gene editing”. By the end, the researchers found that about 6% to 9% of the oocytes, depending on their size, produced offspring with gene-editing events. Around half of the edited lizards held modified genes from both parents. The findings indicate that the CRISPR components remain active for several days, or even weeks, within the unfertilized eggs.

In some other model animals, CRISPR-Cas can have efficiencies up to 80% or higher, which would make the present 6% seem like a paltry amount, Menke explains.

“But no one has been able to do these sorts of manipulations in any reptile before,” he says. “There’s not a large community of developmental geneticists that are studying reptiles, so we’re hoping to tap into exciting functional biology that has been unexplored.”

The team decided to use albinism genes for the study because they result in an obvious physical trait (loss of pigmentation) without being lethal to the animal. Secondly, they wanted to use the lizards as a model to study how the loss of pigmentation impacts retina development, as humans with albinism often have vision problems. The anole lizards are ideally suited for this: their eyes have a fovea, a pit-like structure in the retina that underpins high-acuity vision, which humans share, but most of our main animal models lack.

Ultimately, this gene-editing technique could be translated for use in other animals, Menke adds.

“We never know where the next major insights are going to come from, and if we can’t even study how genes work in a huge group of animals, then there’s no way to know if we’ve explored everything there is to explore in the realm of gene function in animals,” Menke says.

“Each species undoubtedly has things to tell us, if we take the time to develop the methods to perform gene editing.”

The paper “CRISPR-Cas9 Gene Editing in Lizards through Microinjection of Unfertilized Oocytes” has been published in the journal Cell Reports.

Doctors use CRISPR technique for the first time to treat genetic disorder

A group of doctors in the United States has used the powerful gene-editing technique CRISPR to try and treat a patient suffering from a serious genetic disorder. It will take months or even years before knowing whether the treatment is safe and how well it might be helping patients, but doctors are optimistic.

Credit: Flickr

 

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. The term is used to refer to the various systems that can be programmed to target specific stretches of genetic code and to edit DNA and RNA at precise locations, as well as for other purposes, such as for new diagnostic tools.

“It is just amazing how far things have come,” says Victoria Gray, who received the treatment for sickle cell disease. “I always had hoped that something will come along. It’s a good time to get healed.”

Now, researchers have used CRISPR to try and treat a disorder called sickle cell disease.

Sickle cell affects millions of people around the world, causing bone marrow to produce a defective protein that makes blood cells that are sickle-shaped. The deformed cells get stuck inside blood vessels and don’t carry oxygen normally, causing a host of debilitating and, often, eventually life-shortening complications.

“It’s horrible,” Gray said. “When you can’t walk or lift up a spoon to feed yourself, it gets really hard.”

Doctors used cells taken from patients’ own bone marrow that have been genetically modified with CRISPR to make them produce a protein that is usually only made by fetuses and by babies for a short time following birth. Now, the hope is that the protein will compensate for the defective protein that causes sickle cell disease.

“It’s exciting to see that we might be on the cusp of highly effective therapy for patients with sickle cell,” says Dr. David Altshuler, chief scientific officer at Vertex Pharmaceuticals, which conducted the study.

Gray was diagnosed with sickle cell disease when she was an infant. One major symptom is agonizing, debilitating pain. Like many sickle cell patients, her symptoms have prevented her from living a full life. She couldn’t play like other children, was afraid to travel and had to give up her dreams of becoming a doctor or a nurse.

The defective blood cells also increase the risk of infections and damage to vital organs such as the heart. They also can cause life-threatening strokes. Many people with sickle cell disease don’t live past their 40s. Gray’s heart has already suffered damage.

CRISPR enables scientists to make very precise changes in DNA, raising hopes it will lead to new ways to prevent and treat many diseases. Doctors have already started using it to try to treat cancer, mostly in China. At least two patients in the U.S. have been treated for cancer.

Later this year, doctors in Boston are planning to use CRISPR to edit cells in patients’ retinas, in hopes of restoring vision in patients with an inherited form of blindness. But there are challenges ahead.

Frangoul acknowledged there are always risks with experimental treatments. But he says the research will go very slowly and carefully with close review by the Food and Drug Administration and other advisory panels.

“We are very cautious about how we do this trial in a very systematic way to monitor the patients carefully for any complications related to the therapy,” he said.

Credit: Wikimedia Commons.

Scientists treat first US patients with gene-edited cells

Credit: Wikimedia Commons.

Credit: Wikimedia Commons.

CRISPR-cas9, the powerful gene-editing tool, has been getting a bad reputation lately following last year’s shocking news of Chinese twins born with altered genomes. But done diligently and ethically, CRISPR holds the promise to treat some of the most gruesome diseases. At the University of Pennsylvania, scientists have used this technology to make precise DNA modifications to the immune cells of two cancer patients. The ongoing trial marks the first time that CRISPR has been used to treat patients on US soil.

One of the patients has myeloma, and the other one has sarcoma. Both didn’t respond to standard treatment, which is why they agreed to participate in an experimental trial.

CRISPR-Cas9 allows scientists to alter the DNA of different organisms with high speed and precision. It essentially works by injecting a living organism with a DNA construct composed of the Cas9 enzyme that cuts or deletes a segment of DNA, a sequence of RNA that guides the Cas9 to the correct location to cut, and a new DNA template that repairs the cut and alters the gene. Before CRISPR entered the picture, gene editing was a time-consuming and laborious procedure that often ended in failure.

The ongoing trial involves extracting immune system cells, known as T cells, from the blood of the patients, then genetically modifying these cells. The plan is to remove three of the cells’ receptors and to add a gene for a receptor called NY-ESO-1, which is a protein that appears on the surface of some cancers. The modified cells would then be infused into the bodies of the cancer patients after they had received a brief course of chemotherapy.

Ultimately, the researchers hope that the modified cells will target and destroy the cancer cells. So far, no other information has been released to the public but we know that the study will eventually include a total of 18 patients.

Unlike the reckless Chinese experiment that edited the genes of human embryos, the trial involves altering the DNA of individual patients. This means that these modifications will not be passed down the germline so there is no danger of re-engineering the entire human species. Gene-editing of heritable traits is not allowed in the United States and in many other countries.

Besides this trial, a number of research institutes have started or are preparing to start their own CRISPR trials on human patients this year. NPR informs that two trials are underway meant to treat genetic blood disorders, such as sickle cell disease and beta-thalassemia. Another study wants to use CRISPR to treat an inherited form of blindness known as Leber congenital amaurosis. Several other cancer studies are due to kick off this year in Texas, New York and elsewhere.

All of these studies are extremely experimental and the patients involved in them face considerable risks. The biggest concern is that these therapies might cause unintended changes in DNA that could lead to health problems. And even if these preliminary trials are deemed successful, it might take many years before the public gains access to them.

Credit: University of Georgia at Athens.

Scientists use CRISPR to breed albino anole lizards, finally extending the powerful tool to reptiles

Credit: University of Georgia at Athens.

Credit: University of Georgia at Athens.

The powerful gene editing tool CRISPR is all the rage right now. In the future, scientists hope to use this technology to remove malaria from mosquitoes, treat HIV and Alzheimer’s, develop new drugs, and even to create plastics by modifying yeast so that it transforms sugars into hydrocarbons. However, CRISPR (which stands for ‘Clustered Regularly Interspaced Short Palindromic Repeats’) didn’t seem to work on lizards and snakes. But researchers at the University of Georgia in Athens thought outside the box egg and devised a workaround that finally brings the mighty gene editing tool to the worlds of reptiles.

CRISPR-Cas9 allows scientists to alter the DNA of different organisms with high speed and precision. It essentially works by injecting a living organism with a DNA construct composed of the Cas9 enzyme that cuts or deletes a segment of DNA, a sequence of RNA that guides the Cas9 to the correct location to cut, and a new DNA template that repairs the cut and alters the gene. Before CRISPR entered the picture, gene editing a time-consuming and laborious procedure that often ended in failure.

“CRISPR-Cas9 mediated gene editing has enabled the direct manipulation of gene function in many species. However, the reproductive biology of reptiles presents unique barriers for the use of this technology, and there are currently no reptiles with effective methods for targeted mutagenesis,” the authors wrote.

Typically, researchers edit the genes of an organism by injecting the DNA construct into a single-celled fertilized egg, thus leading to a genomic alteration that is present in all subsequent cells. This approach, however, doesn’t work on female anoles, which store sperm in their oviducts for long periods of time. This makes it virtually impossible to properly time CRISPR injection to fertilization. What’s more, the females also form eggshells at fertilization and inserting a needle at this point can damage the embryo.

The researchers at the University of Georgia solved this challenge by inserting the CRISPR complex into unfertilized eggs still in the ovaries. For their experiment, the authors targetted a gene that produces an enzyme that controls pigmentation. The team altered a total of 146 immature eggs from 21 lizards, resulting in the breeding of four albino offspring.

Scientists claim that the new method should work for other species of lizard as well as snakes, making it a true game-changer in the field.

The results were posted in the preprint server bioRxiv.

Chip combining CRISPR and graphene can detect genetic mutations in minutes

Two of the most promising novel techniques have been used together with remarkable results. US researchers have combined CRISPR with electronic transistors made from graphene to create a new hand-held device that can detect specific genetic mutations in a matter of minutes.

“We have developed the first transistor that uses CRISPR to search your genome for potential mutations,” said Kiana Aran, an assistant professor at KGI who conceived of the technology while a postdoctoral scholar in UC Berkeley bioengineering professor Irina Conboy’s lab. “You just put your purified DNA sample on the chip, allow CRISPR to do the search and the graphene transistor reports the result of this search in minutes.”

The novel system immobilizes the CRISPR complexes on the surface of graphene-based transistors. These complexes search a genome to find their target sequence and, if the search is successful, bind to its DNA. This binding changes the conductivity of the graphene material in the transistor, which picks the change and relays it to a handheld reader. Image credits: Keck Graduate Institute (KGI).

Genetic scissors

Genetic analysis has developed tremendously in recent years. Not only has it become a relatively common scientific and medical practice, but commercial companies are even offering genetic tests readily available to customers. Over 20 million have already reportedly taken at-home genetic tests.

When these tests are looking for genetic mutations, they “amplify” the DNA segment of interest millions of times to have a better look at it. This process (called polymerase chain reaction or PCR) is time and equipment-intensive, which means that samples have to be sent to a lab and subjected to analysis by expensive and delicate equipment. This is where CRISPR and graphene enter the scene.

The CRISPR-Cas9 system brought in an unprecedented precision, allowing researchers to snip threads of DNA at very precise locations — something often called “genetic scissors.”

“CRISPR-Chip has the benefit that it is really point of care, it is one of the few things where you could really do it at the bedside if you had a good DNA sample,” said Niren Murthy, professor of bioengineering at UC Berkeley and co-author of the paper. “Ultimately, you just need to take a person’s cells, extract the DNA and mix it with the CRISPR-Chip and you will be able to tell if a certain DNA sequence is there or not. That could potentially lead to a true bedside assay for DNA.”

But in order for it to work its magic, the Cas9 protein needs to first locate the spots it needs to cut. Graphene, a single atomic layer of carbon, is extremely electrically sensitive and small enough for this type of application. Researchers attached a deactivated Cas9 protein (one which finds the targeted DNA segment, but doesn’t cut it) and tethered it to transistors made of graphene. When the protein finds the spot, it binds to it and triggers a change in the electrical conductance of the graphene. In turn, this changes the characteristics of the transistors, and this change can be detected with a hand-held device. Ultimately, this allows the detection of genetic mutations within minutes, using relatively simple equipment, in less than an hour.

“Graphene’s super-sensitivity enabled us to detect the DNA searching activities of CRISPR,” Aran said. “CRISPR brought the selectivity, graphene transistors brought the sensitivity and, together, we were able to do this PCR-free or amplification-free detection.”

The handheld device. Image credits: Keck Graduate Institute.

To demonstrate the equipment’s potential, researchers analyzed blood samples from patients suffering from Duchenne muscular dystrophy (DMD). DMD is a genetic disorder characterized by progressive muscle degeneration and weakness — one of nine known types of muscular dystrophy. Diseases such as DMD are thought to be caused by mutations throughout the dystrophin gene — but this is one of the longest in the human genome and spotting mutations can be costly and time-consuming using PCR-based genetic testing. This is where the novel CRISPR/graphene technology can make a huge difference.

“As a practice right now, boys who have DMD are typically not screened until we know that something is wrong, and then they undergo a genetic confirmation,” said Conboy, who is also working on CRISPR-based treatments for DMD.

“With a digital device, you could design guide RNAs throughout the whole dystrophin gene, and then you could just screen the entire sequence of the gene in a matter of hours. You could screen parents, or even newborns, for the presence or absence of dystrophin mutations — and then, if the mutation is found, therapy could be started early, before the disease has actually developed.”

Researchers also say that things can be scaled up to the point where a handheld device would scan for multiple genetic disorders at the same time. Rapid genetic testing could also be used to help doctors develop individualized treatment plans for their patients, Murthy said. For example, genetic variations make some people unresponsive to expensive blood thinners, like Plavix.

Rapid genetic testing could also be used to help doctors develop individualized treatment plans for their patients, Murthy said. For example, genetic variations make some people unresponsive to expensive blood thinners, like Plavix.

“If you have certain mutations or certain DNA sequences, that will very accurately predict how you will respond to certain drugs,” Murthy concludes.

The study has been published in nature biomedical engineering

He Jiankui. Credit: Wikimedia Commons.

The rogue Chinese scientist who made the first gene-edited human babies could face death penalty

He Jiankui. Credit: Wikimedia Commons.

He Jiankui. Credit: Wikimedia Commons.

He Jiankui, the controversial scientist whose unlicensed work led to the birth of twin baby girls whose DNA was modified, is in big trouble. Since his announcement sparked international outcry, the Chinese scientist has come off the radar. According to sources close to the matter, He Jiankui has been under armed guard at a state-owned apartment in Shenzen, China, since early December. The scientist is now facing corruption and bribery charges, both crimes that carry the death penalty in China.

A scapegoat?

The Chinese researcher, who used to be an Associate Professor at Southern University of Science and Technology, in Shenzhen, used CRISPR gene-editing technology to modify live embryos. The procedure allegedly modified the CCR5 gene in such a way as to potentially make the offspring resistant to HIV. Instead of destroying the embryos, per research guidelines in China, He Jiankui and associates planted the embryos in surrogate mothers and allowed the pregnancy to follow through, resulting in the birth of twin baby girls. The birth has not been independently confirmed or documented in a peer-reviewed journal, but respectable researchers with access to some of He’s work say in all probability the work was carried through

The announcement was made quite nonchalantly by He during a keynote presentation at the Second International Summit on Human Genome Editing at the University of Hong Kong, held in November 2018. One of the organizers, geneticist Robin Lovell-Badge of the Francis Crick Institute in London, had invited He to speak at the conference after learning of his plans. Lovell-Badge had hoped that attending the conference with some of the foremost people in the field would temper the Chinese scientist’s enthusiasm. But much like everybody else at the event, Lovell-Badge was flabbergasted to learn that He wasn’t just planning — the work had already been done.

“None of us knew how far he’d actually got,” Lovell-Badge said, adding that experts knew only of his research on mice, monkeys and human embryos. “Clearly, we were too late.”

Subsequently, we came to learn that He had been working on his research while on unpaid leave and used his own financial resources to hire people to help him. He had founded and sold various companies which made him very wealthy and respected (until recently) by Chinese elites. Although the documents the Chinese researchers filed for clinical trials included a valid ethical review, the hospital involved denied that its ethics review committee ever met to discuss the work. China’s Southern University, where He and colleagues were employed, said it did not support the experiment. The university also announced that it has launched an investigation. To make matters worse, He is a trained physicist with little to any experience in biology.

What’s striking is that the 34-year-old scientist had no sense of remorse while making his ‘big’ announcement in Hong Kong. He actually said that he was proud of the achievement.

Well, it seems that Chinese authorities are of a different opinion.

Speaking to The Telegraph, Lovell-Badge said He could face corruption and bribery charges, adding that “quite a few people have lost their heads for corruption.” Indeed, things look pretty gloomy for He Jiankui, who was expecting reverence as a pioneer, but who instead could face the axe.

“Lots of people are probably going to lose their jobs, he wasn’t the only one involved in this obviously. So how has he got them to do all this work? He could be had up on all sorts of charges of corruption and being guilty of corruption in China these days is not something you want to be,” Lovell-Badge told The Telegraph.

“Here you have a physicist who knows little biology, is very rich, has a huge ego, wants to be the first at doing something that will change the world,” Lovell-Badge added.

Lovell-Badge says that He is currently confined to an apartment under armed guard. It’s not clear at this point if the guards are there to restrict him or protect him. Since He made his controversial announcement, the Chinese physicist has received many death threats.

For the moment, He is under investigation by the Chinese government and could face jail time or even the death penalty, in the most extreme case. It’s an incredibly opaque situation at this point, as with many dark things in China. It would be very convenient for the local authorities to present a scapegoat — the head on a pike that eases the anger of the masses. However, what’s to keep something similar from happening again? If there’s anything to learn from this whole scandal it is that all countries should require stricter oversight and laws around gene editing on humans.

He Jiankui is a Chinese biomedical researcher, who was trained in the United States. He became widely known in November 2018 after he said that he had generated the first human genetically edited babies, Lulu and Nana. Credit: Wikimedia Commons.

China pulls the plug on rogue scientist who genetically modified twin human babies

He Jiankui is a Chinese biomedical researcher, who was trained in the United States. He became widely known in November 2018 after he said that he had generated the first human genetically edited babies, Lulu and Nana. Credit: Wikimedia Commons.

He Jiankui is a Chinese biomedical researcher, who was trained in the United States. He became widely known in November 2018 after he said that he had generated the first human genetically edited babies, Lulu and Nana. Credit: Wikimedia Commons.

Everyone was completely taken by surprise when, earlier this week, a Chinese scientist announced that he had used gene-editing technology to alter the genes of twin girls. The lack of transparency and gross lack of oversight, ethical or otherwise, attracted widespread international scrutiny. Today, the Chinese government announced that it had ordered a temporary halt on research for all personnel involved with the controversial gene-editing technique.

No shame, no remorse

He Jiankui, an Associate Professor at Southern University of Science and Technology, in Shenzhen, had announced that twin baby girls born this month had their embryonic genes edited using CRISPR technology. The Chinese researchers modified the CCR5 gene in such a way as to potentially make the offspring resistant to HIV.

The major concern is that any edits will be passed onto offspring, thus making their way into the gene pool. As such, potentially troublesome mutations could become relatively widespread. On the other hand, even if the gene editing process is flawless, any beneficial gene edits — such as enhanced resistance to disease and even intelligence — could result in unfair advantages and may open the door for eugenic practices.

“If true, this experiment is monstrous,” said Julian Savulescu, a professor of practical ethics at the University of Oxford. “The embryos were healthy. No known diseases. Gene editing itself is experimental and is still associated with off-target mutations, capable of causing genetic problems early and later in life, including the development of cancer.”

“There are many effective ways to prevent HIV in healthy individuals: for example, protected sex. And there are effective treatments if one does contract it. This experiment exposes healthy normal children to risks of gene editing for no real necessary benefit. In many other places in the world, this would be illegal punishable by imprisonment.”

Germline gene editing is banned in many countries. However, while it is not allowed per se, China does not stipulate any punishments for the practice.

Few people were aware that such work was being practiced, which certainly didn’t help calm down the scientific community. Some people hoped that He hadn’t really messed with the genomes of live human babies, since the research was not independently verified by a third party or peer-reviewed. However, all signs point to the fact that the procedure was indeed carried out. On Wednesday, He presented his work in great detail at the Second International Summit on Human Genome Editing in Hong Kong. At the end of the presentation, He stated he was proud of what he had done.

Speaking to New Scientist, Helen O’Neill, a CRISPR specialist at the University College London who attended the conference, said that the Chinese researchers really did it.

“Among the scientific community, we’re very sure. He gave quite an impressive presentation on quite extensive and thorough research that he had done both in animal and human embryos. The initial shock meant people went “Surely not – he has to prove it.” But I never had any doubt,” she said.

There are a number of very odd things about this whole affair. He has been off the radar for months, working on his research while on unpaid leave. Although the documents the Chinese researchers filed for clinical trials included a valid ethical review, the hospital involved denied that its ethics review committee ever met to discuss the work. China’s Southern University, where He and colleagues are employed, said it did not support the experiment. The university also announced that it has launched an investigation.

“The research work was carried out outside the school by Associate Professor He Jiankui. He did not report to the school and the department of biology, and the school and the biology department did not know about it,” a spokesperson from the university said in a statement.

The backlash following the most controversial (and some would say scandalous) research of the year was extremely intense. Following international outcry, the Health Ministry, Science and Technology Ministry and China Association for Science and Technology stated that “relevant bodies have been ordered to temporarily halt the scientific research activities of relevant personnel.”

The organizers of a conference where He announced the live gene editing also condemned the work, calling it “deeply disturbing” and “irresponsible.”

“Even if the modifications are verified, the procedure was irresponsible and failed to conform with international norms,” read a statement from the Second International Summit on Human Genome Editing,

These sentiments were shared by colleagues in the United States.

“The events in Hong Kong this week clearly demonstrate the need for us to develop more specific standards and principles that can be agreed upon by the international scientific community,” U.S. National Academy of Sciences (NAS) president Marcia McNutt and  U.S. National Academy of Medicine (NAM) president Victor Dzau said in a joint statement.

What’s shocking is that the twin baby girls will not be alone. Very casually, He announced during a Q&A at his keynote at this week’s Hong Kong conference that another CRISPR pregnancy is underway.

No one knows what will happen next. It’s simply unprecedented to have so many written and unwritten rules broken repeatedly. One thing’s for sure, all of this shaping up to be a huge disaster. He’s career looks like it’s going down the drain — but that should be the least of anyone’s worry. The real challenge now is preventing a biological meltdown and making sure nothing so reckless is allowed to ever happen again.

Chinese scientists created the world’s first gene-edited babies

A group of Chinese researchers recruited couples in order to create the first gene-edited babies — a pair of twin girls born earlier this month. The controversial initiative aims to make babies resistant to certain diseases and pathogens, such as HIV infections.

The news was first reported by MIT Technology Review, which obtained official medical documents (1 and 2) filed by researchers at the Southern University of Science and Technology, in Shenzhen.

According to the documents, the Chinese researchers want to use the gene-editing tool CRISPR to modify human embryos and then transfer them into women’s uteruses. They plan to edit the CCR5 gene in such a way as to potentially make the offspring resistant to HIV, smallpox, and cholera. Using the

The team led by He Jiankui previously carried out tests on fetuses as late as 24 weeks, or six months, into the pregnancy. Their first tests on human embryos in a dish were carried in 2015, causing an ethical debate among the scientific community.

Although gene editing on humans is prohibited in most countries (China has banned cloning but not human embryo gene editing specifically), He and colleagues seem nevertheless bent on experimenting with gene editing and human cells. The major concern is that any edits will be passed on to offspring, thus making their way into the gene pool. As such, potentially troublesome mutations could become relatively widespread. On the other hand, even if the gene editing process is flawless, any beneficial gene edits — such as enhanced resistance to disease and even intelligence — could result in unfair advantages and may open the door for eugenic practices.

Jiankui He. Credit: SOUTHERN UNIVERSITY OF SCIENCE AND TECHNOLOGY.

It’s all uncharted territory, and the long-term consequences of gene editing on humans can be unpredictable, which is why the scientific community advises caution. In stark contrast to this cautionary approach, He claimed that his team has “a strong responsibility that it’s not just to make a first, but also make it an example.”

He says that the aim of the trial is not to cure or prevent an inherited disease, but rather to bestow traits that few people naturally have. Specifically, the ability to resist an infection with HIV, which some individuals from Western European populations have due to a rare CCR5 genetic mutation. This gene forms a protein doorway that allows HIV, the virus that causes AIDS, to enter a cell; the mutation alters this doorway, physically blocking the virus from entering the cell.

According to the Associated Press, the Chinese researchers have altered embryos for seven couples during fertility treatments, with one pregnancy being carried to term thus far. All the men involved in the trial had HIV, while the women did not. This claim, however, is unverified, and the work has yet to be published in any journal.

The gene editing occurred during the lab dish fertilization (IVF) stage. The researchers first separated sperm from semen, the fluid which may contain HIV. A single sperm cell was joined with a single egg to form an embryo, which was subjected to gene editing via CRISPR. Once the embryos were 3 to 5 days old, some cells were removed and checked for editing. Overall, the Chinese researchers edited 16 of 22 embryos, out of which 11 embryos were used in six implant attempts, resulting in a single twin pregnancy. The couples could choose whether to use edited or unedited embryos for their pregnancy attempts.

Tests suggest that one twin had both copies of the altered gene and the other twin had just one altered copy. There was no evidence that suggests harm to other genes, according to He. People with only one copy of the CCR5 gene can still get HIV. Further pregnancies are on hold until the twin pregnancy is deemed safe.

Ground cherry

In a just a few years, scientists could domesticate the delicious ground cherry

Move over, strawberry — there’s a new berry in town that Millenials are drooling over. Using state-of-the-art gene editing, researchers claim they’ve come close to domesticating the groundcherry, a wild berry native to Central and South America. Instead of waiting for decades or even thousands of years to domesticate the berry through conventional methods, the scientists say that their approach could bring this highly-sought-after food to supermarket shelves around the world much faster.

Ground cherry

Credit: Pixabay.

The ground cherry (Physalis pruinosa) is classed as an orphan crop — minor crops, which also includes tef, finger millet, yam, roots, and tubers, that tend to be regionally important but not traded around the world. The reason why such foods are rarely traded internationally is due to their poor shelf life and low productivity.

Sometimes called cape gooseberries, winter cherries, or husk tomatoes, ground cherries are small yellow fruits with a papery husk. Their taste has been described as something between a tomato and pineapple, which makes them great as ingredients in desserts, salads, jams, or even plain.

Ground cherries sometimes make their way into U.S. farmers markets where they sell like hotcakes. In order to make them more available to consumers, the orphan crop would have to be grown more easily and with a much higher yield. Typically, we’d have to wait for many years to completely domesticate the plant. However, researchers at the Boyce Thompson Institute decided to take a shortcut.

Researchers managed to bring the ground cherry from almost wild to almost domesticated in a matter of years. Credit: Sebastian Soyk.

Researchers managed to bring the ground cherry from almost wild to almost domesticated in a matter of years. Credit: Sebastian Soyk.

The team wanted to make the plant’s weedy shape more compact, give it larger fruits and more prolific flowers. First, they sequenced the ground cherry’s genome, which enabled them to identify the genes responsible for the crop’s undesirable traits. Then, the researchers used the controversial gene editing tool CRISPR to manipulate these target genes.

“I firmly believe that with the right approach, the groundcherry could become a major berry crop,” said Zachary Lippman, a plant scientist at Cold Spring Harbor Laboratory.

“I think we’re now at a place where the technology allows us to reach.”

Previously, the team manipulated the genomes of certain tomatoes — an approach which they applied to the ground cherry as well.

For now, the project is a proof of concept — the first orphan crop in which CRISPR was applied to make it a ‘family’ crop that has a high yield. In the future, the researchers plan on fine-tuning their method to improve desired characteristics, such as fruit color and flavor. Of course, some conventional plant breeding will be required in order to make the ground cherry mainstream. How long this will take is not clear, as there is also the issue of navigating CRISPR’s intellectual property rights.

In any event, Lippman says that the study is all about “demonstrating what’s possible”, such that other researchers might be inspired to take on other orphan crops that have the potential for rapid domestication. This way, food security will be improved and our plates can be enriched with new flavors and tastes.

The findings appeared in the journal Nature Plants.

Wings

CRISPR was used to change a butterfly’s wing color

Butterflies have complex color and scale patterns that allow them to camouflage, attract mates, or warn predators. Researchers used CRISPR/Cas9 to study the genes of one butterfly species to see how they contribute to the wing color and scale structure. Surprisingly, they found that the scale and color of the wings are linked to the same genes.

Wings

The wings of each melanin gene mutant.
image credits

The squinting bush brown butterfly, Bicyclus anynana, comes from East Africa and is typically a dark brown color. A postdoctoral fellow at the National University of Singapore, Yuji Matsuoka, disabled five of the butterfly’s pigment genes with CRISPR/Cas9. CRISPR is a new gene editing system that is capable of adding and disabling genes to different organisms easily and cheaply. The mutations not only changed the color of the butterfly to a light brown/yellow, but also altered the wing scale structure.

“Our research indicates that the color and structure of wing scales are intimately related because pigment molecules also affect the structure of scales,” says senior author Antónia Monteiro, a biologist at the National University of Singapore’s Faculty of Science and Yale-NUS College in Singapore. “Some end products of the melanin pathway, which produces butterfly wing pigments, play a role in both scale pigmentation and scale morphology.”

One mutation prevented the manifestation of the pigment dopa-melanin and it also caused an extra sheet of chitin to form horizontally on the upper surface of the wing scale. However, when the different pigment dopamine-melanin was mutated, there were suddenly vertical blades of chitin. This work shows that butterfly color and scale structure are intimately linked and seem to work together. These fives genes could constrain the evolution of a butterfly’s color.

The wildtype butterfly (left) and with mutations (right).
Image credits: William H. Piel and Antónia Monteiro.

The morphology of wing scales is very different between butterfly species. Melanin seems to be an important molecule in this process and it is likely not the only one. These results also help us to know more about the development and evolution of butterfly wing scales.

“Some butterflies can have vivid hues just by having simple thin films of chitin on their scales that interfere with incoming light to create shades known as structural colors without producing corresponding pigments,” says Monteiro. “Light beams reflecting off the top and bottom surfaces of the chitin layer can interfere with each other and accentuate specific colors depending on the thickness of the film, so our results might be interesting in this context.”

One interesting application of this result could be to bioengineer bright colors based on butterfly scales in the future. Above all, this discovery helps us to better understand butterfly coloration and wing scale structure.

Journal reference: Matsuoka et al. 2018. Melanin Pathway Genes Regulate Color and Morphology of Butterfly Wing Scales. Cell Reports.

A CRISPR protein targets specific sections of DNA and cuts them. Credit: Univ. of Texas at Austin.

CRISPR gene editing might cause cancer — but scientists say we shouldn’t panic

A CRISPR protein targets specific sections of DNA and cuts them. Credit: Univ. of Texas at Austin.

A CRISPR protein targets specific sections of DNA and cuts them. Credit: Univ. of Texas at Austin.

CRISPR-Cas9 is a customizable tool that lets scientists cut and insert small pieces of DNA at precise areas along a DNA strand. Its widely heralded for its potential to completely disrupt the biotech industry, with huge impacts from everything from GMO crops to, perhaps, human health.

Two new studies, however, are causing a stir after they found the technology could cause cancer in human cells. But despite media coverage framing the findings as a cause for concern, the authors themselves are far more reserved, stating “reactions have been exaggerated.”

One of the studies was carried out by researchers at Novartis, a private pharmaceutical firm, one of the few that has a gene-editing therapy approved by the FDA. The other was published by researchers at the Karolinska Institute, Sweden.

Both research studies independently found evidence that the p53 gene either blocks CRISPR from working properly in human cells or breaks apart during the molecular procedure. This gene is responsible for repairing DNA or, failing that, it can tell a cell to die — both are effective ways of preventing cancer. A defective p53 gene can thus cause cancer. Previous studies have associated defective p53 genes to several cancers like those affecting the breast, lung, ovaries, stomach, colon, and pancreas.

The news caused a wave of panic, hitting some biotech companies hard. Quartz informs that Crispr Therapeutics AG, based in Switzerland, and Intellia Therapeutics Inc, based in the US state of Massachusetts, saw their stocks drop 12.6% and 9.8%, respectively, only one day after the studies were published.

The authors of the studies themselves are not worried, however. Why? For one, just because something occurs at the cellular level, that doesn’t necessarily translate at the macro-level, in the living body. Secondly, there are other proteins besides Cas9 that can be used to cut DNA. Another protein, Cpf1, can be used instead of Cas9, which is even simpler and more precise. Perhaps, future studies will find those proteins that do not interfere with p53 gene expression at all, thereby dispelling any concerns.  

Ultimately, before a study shows that a CRISPR-edited animal model has higher-than-expected cancer rates, the gene editing tool is still fair game. Of course, the two studies should make scientists act with caution in the future. At the same time, the takeaway is that CRISPR is still an extremely promising technology with no major safety concerns identified so far.

Both studies appeared in the journal Nature (1 and 2). 

Making babies on Mars will be challenging and might even lead to a new species of humans

Credit: Wikimedia Commons.

If Elon Musk ever has his way, humans could settle Mars as early as 2024. The goal is to move our earthling butts to another planet and finally become an interplanetary species, one less vulnerable to extinction. In the process, however, we might actually be triggering the rapid evolution of a new species that is more adapted to the alien environment — in this case, Mars. That’s what a recent study seems to hint at, listing some of the risks people trying to conceive on Mars might face and discussing some of the ethical implications that arise from it.

Would you raise your kids on Mars?

In many respects, the fourth planet from the sun is pretty Earth-like. However, while it was once home to flowing rivers and oceans of water, today the Red Planet is barren and inhospitable to life, despite our biggest hopes that one day we might find life there or at least some evidence of past life.

Both NASA and the famous SpaceX CEO Elon Musk want to establish a permanent colony on Mars at some point. This means that settlers there will also have to have babies in order to expand the colony. However, with its freezing temperature, thin atmosphere, low gravity, and a slew of other perils, Mars isn’t exactly the nicest place to raise children. Actually, according to a new study published in the journal Futures, it will be quite the ordeal.

“Reproduction on Mars will be necessary for colony survival and subsequent expansion,” the team of researchers wrote the new paper. “Unfortunately, such an endeavor comes with titanic challenges.”

The average temperature on Mars is about -80 degrees Fahrenheit (-60 degrees Celsius), although it can vary from -195 F (-125 C) near the poles during winter to as much as 70 F (20 C) at midday near the equator. The carbon-dioxide-rich atmosphere of Mars is also roughly 100 times less dense than Earth’s on average, but it is nevertheless thick enough to support weather, clouds, and winds. A thin atmosphere means much more radiation from the sun reaches Mars’ surface than on Earth. This increases the risk of developing brain cell damage and various cancers. And concerning reproduction, it will also severely impact sperm count. Some of these radiation effects may be offset if the colony is located deep under the Martian surface — but it’s unclear at this point how safe humans would be in such conditions.

Mars also has a much weaker gravity than on Earth, about a third of we’re used to. This means that there’s far less pressure and stress on the human body, which sounds like good news. The problem is that this sudden change in gravity will impact human health, as previous studies on astronauts stationed to the ISS have shown. Altered vision and increased pressure inside the head are among the physiological changes both men and women experience following space flight. These symptoms have been lumped together by NASA under the ‘visual impairment intracranial pressure syndrome’, or VIIP syndrome for short. Scientists hypothesized that at least one of the causes for VIIP syndrome could be related to the redistribution of body fluid toward the head due to microgravity exposure.

Microgravity also seems to change the brain structure of astronauts. Although Mars has some gravity, it’s conceivable that it could have similar effects on colonists’ health — albeit to a less degree than on the ISS — since it’s much lower than Earth’s. What’s more, babies born on Mars would face huge problems adjusting to Earth, if they ever decide to travel there. For example, one NASA scientist, Al Globus, gives an example of someone who weighs 160 pounds. “If I went to a 3g planet, the equivalent of moving from Mars to Earth, I would weigh almost 500 pounds and would have great difficulty getting out of bed,” Globus told Live Science in 2011.

Some might interject that many of these issues can be solved with technology: We can build better shelters and, at the end of the day, Martian settlers will just have to alter their babies’ genome in order for them to adapt to alien conditions. But this would entail a set of ethical and social challenges the likes of which humans have never before experienced. It could mean that some people would simply not be allowed to have kids, for instance. Also, in a very resource-limited Martian society, very weak or ‘useless’ individuals might have to be discarded for the greater good of the colony.

“The idea to protect life at every stage of development may not be suited to a Mars colony,” the authors wrote. “An inhospitable environment and a small mission crew may result in the elevation of the value of group over the individual.”

“The method of CRISPR makes possible adaptive genetic engineering,” the authors wrote. “We should consider the idea of genetic human enhancement before and during that mission.”

In doing so, however, we might end up creating a new species of humans.

For centuries, ever since the first astronomers turned the first rudimentary telescopes towards Mars, mankind has imagined encountering Martians. Ironically, these fabled Martians might just end up being a new race of Earthlings.

DNA structure.

CRISPR-Cas9 scissors can cut through both DNA and RNA

DNA structure.

Image: public domain.

CRISPR-Cas9 technology has the potential to dramatically alter our environment and livelihoods. This powerful tool can cut out portions of DNA — the molecule that contains the blueprint of life — with such precision that unwanted genes, and only those genes, can be removed from the genome.

The possibilities are virtually endless. Using CRISPR-Cas9, scientists can engineer crops faster and more efficiently than ever or even potentially eradicate genetic diseases in humans. It’s even spilled over into the designer babies topic, starting a whole ethical debate regarding the use of CRISPR.

Now, scientists in Germany have shown that the genetic slicing tool can also target RNA, with potentially far-reaching ramifications.

The molecular scissor

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. Gene editing with CRISPR-Cas9 is still in its infancy despite its widespread use among the world’s foremost research institutes. It was only a couple years ago that scientists discovered that the foodborne pathogen Campylobacter jejuni has an ingenious immune system that recognizes and deletes foreign genomic material from invading viruses, protecting the bacteria’s genetic integrity.

Its immune system performs this feat with the help of guide-RNA, which leads the Cas9 protein to the site of foreign viral material. Once there, Cas9 targets and cuts the DNA. The guide-RNA and Cas9 can be pictured as a hand and scissors. Using artificial guides, scientists have been able to modify specific genes in bacteria, but also in plants and animals. There are already thousands of peer-reviewed papers focusing on CRISPR technology.

Researchers at the Julius-Maximilians-Universität Würzburg (JMU) and the Helmholtz Institute for RNA-based Infection Research (HIRI) recently showed that the CRISPR-Cas9 system isn’t limited to desoxyribonucleic acid (DNA). Instead, the protein can also target and cut related molecules such as ribonucleic acids (RNA).

“The finding was surprising, given that Cas9 is thought to naturally target DNA only,” said Prof. Chase Beisel, a researcher at HIRI and co-author of the new study, in a statement.

“We continue to be astounded by the many things that Cas proteins are capable of. They can target DNA, they can target RNA, they can target both at the same time. They can also do different things upon target recognition, such as activating domains that cleave any DNA or RNA they find or produce small molecules that can diffuse and interact with other proteins,” Beisel told ZME Science in an e-mail.

Due to its phenomenal versatility, Beisel likens Cas proteins to a swiss army knife. However, it wasn’t easy for the researchers to unlock this new capability.

“One of the challenges was that virtually all of the RNAs bound by Cas9 in Campylobacter jejuni exhibited only partial complementarity between the guide RNA and the bound RNA. There were few trends to predict which RNAs would be bound and then which would be cleaved. However, our moment of validation was designing synthetic guide RNAs and showing that they could predictably bind and cleave a target unrelated to any of the RNAs identified in Campylobacter,” Beisel said.

From the left: Prof. Dr. Cynthia Sharma, Sara Eisenbart, Thorsten Bischler, Belinda Aul from the Institute of Molecular Infection Biology (IMIB) and Prof. Dr. Chase Beisel from the Helmholtz-Institute of RNA-based Infection Research (HIRI) in Würzburg. Credit: Hilde Merkert, IMIB.

RNA is DNA’s discount cousin, but equally indispensable for life. Whereas DNA is double-stranded (the famous double helix), RNA is single-stranded. RNA’s primary role is to act as a messenger of genetic material within the cell. For instance, genes — information stored in DNA — are transcribed into RNA, which then serves as a template for the translation of the gene’s information into proteins. The ability to target both RNA and DNA with laser precision gives scientists access to all sorts of new opportunities, from controlling which genes are turned on or off, to annihilating RNA viruses.

This isn’t the first study that found Cas proteins can target RNA. Last year, two other research group reported similar findings, intriguingly using two different bacteria. This means that RNA-targeting is a general trait of the Cas9 protein, independent of the bacteria species from which it is sourced. What’s more, this new study goes a step forward because it uses Cas proteins that can target both DNA and RNA, which is a first, while the previously mentioned studies focused on proteins that exclusively targetted RNA, not DNA.

“This prior study worked with a different Cas protein called C2c2 (or Cas13a). This differs from our Cas9 protein because C2c2 only targets RNA, whereas our protein has the ability to target both DNA and RNA. In addition, C2c2 requires the presence of a flanking sequence, so it cannot target any sequence, whereas our protein did not have any requirements when targeting RNA,” Beisel wrote.

In the future, the researchers plan on investigating whether the CRISPR-Cas9 system plays others roles, apart from combating infection, in Campylobacter. For instance, is it also involved in turning genes on and off in the bacteria? The answer to this and other questions might reveal even more amazing insights about the most powerful genetic tool in our arsenal.

“Our work and that of other groups continue to find new capabilities — the equivalent of additional attachments within the swiss army knife — and I imagine that other capabilities await discovery,” Beisel concludes on an excited tone.

Scientific reference: Gaurav Dugar, Ryan T. Leenay, Sara K. Eisenbart, Thorsten Bischler, Belinda U. Aul, Chase L. Beisel, Cynthia M. Sharma: CRISPR RNA-dependent binding and cleavage of endogenous RNAs by the Campylobacter jejuni Cas9; Molecular Cell, DOI: https://doi.org/10.1016/j.molcel.2018.01.032.