CRISPR system scales up in human cells

By Haley Bridger, 

Broad Communications, 

December 12th, 2013

The CRISPR-Cas9 system causes a precise double strand break in DNA, which leads to a gene being turned off. Researchers have scaled up to turn off genes accurately and efficiently at a genomic scale instead of just one or a few genes at a time.

For decades, researchers have sought a biological toolset capable of precisely and systematically turning off genes throughout the genomes of human cells. The CRISPR-Cas9 system – a recently discovered system with bacterial origins – has the potential to overcome many of the limitations of currently available gene-silencing techniques. Earlier this year, several research groups showed that it was possible to use CRISPR-Cas9 to turn off genes in mammalian cells.

But in order to investigate and better understand the genetics of health and disease, scientists need a toolset that can reliably turn off each of the genes in the genome on a large scale.

In companion papers published together this week in Science, researchers from the Broad Institute, Whitehead Institute, McGovern Institute for Brain Research, and elsewhere have scaled up, demonstrating the capabilities of the CRISPR-Cas9 system in large-scale studies of several types of human cells, turning off genes accurately and efficiently at a genomic scale instead of just one or a few genes at a time. The two papers – which offer up libraries of tens of thousands of complexes tailored to match precise locations throughout the genome – lay the groundwork for a range of future studies, including investigations into neural development, cancer, and many other human diseases.

“We can now use this technology on a genome-wide scale, giving us the ability to interrogate any gene we want,” said Feng Zhang, a core member of the Broad Institute, an investigator at the McGovern Institute, and an assistant professor at MIT. Zhang is also the senior author of one of theScience papers. “Additionally, we demonstrate the utility of CRISPR for making biological discoveries, identifying new genes likely involved in how cancer cells become resistant to treatment. This is likely the first biological discovery made using CRISPR.”

Unlike other gene-silencing tools, the CRISPR-Cas9 system targets the genome’s source material: while RNA interference (RNAi) must target many copies of messenger RNA in order to tamp down a gene’s expression, CRISPR-Cas9 permanently turns off genes at the DNA level. The CRISPR-Cas9 system includes an enzyme that makes a cut in DNA, and is paired with a single guide RNA (sgRNA), which researchers construct to home in on a specific site in the genome. The DNA cut – known as a double strand break – closely mimics the kinds of mutations that occur naturally, for instance after chronic sun exposure. But unlike the UV rays that can result in genetic alterations, the CRISPR-Cas9 system causes a mutation at a precise location in the genome.

When cellular machinery repairs the DNA break, it removes a small snip of DNA, rendering a gene non-functional. In this way, researchers can precisely turn off specific genes in the genome.

To turn off genes on a grand scale, both sets of investigators developed libraries of more than 65,000 sgRNAs. The library from Zhang’s group is designed to target almost every protein-coding gene in the genome.

Both research teams used CRISPR-Cas9 to study the development of resistance to drugs used to treat cancer. The research team from the Whitehead and the Broad investigated genes whose loss conferred resistance to etoposide, a drug used to treat many forms of cancer including lung cancer and testicular cancer. The Broad and McGovern researchers used CRISPR-Cas9 to find genes involved in resistance to a drug commonly used to treat melanoma. In both sets of experiments, the research teams uncovered several previously unknown genes tied to resistance as well as many established genes.

In addition to these experiments on resistance, the researchers also conducted several other studies, using the CRISPR-Cas9 system in human pluripotent cells and cells grown in different culture conditions. The CRISPR-Cas9 system proved effective across these cell types, further demonstrating its versatility.

“With this work, it is now possible to conduct systematic genetic screens in mammalian cells,” said David Sabatini, a member of the Whitehead, professor of biology at MIT, investigator of the Howard Hughes Medical Institute, senior associate member at the Broad, and a member of the Koch Institute. Sabatini is also a co-senior author of one of the Science papers. “This will greatly aid efforts to understand the function of both protein-coding genes as well as non-coding genetic elements.”

The research teams compared the results of using the CRISPR-Cas9 system to turn off genes to the effectiveness of RNAi to turn down the signal of genes. In general, RNAi only partially reduces a gene’s signal – knocking it down – while CRISPR-Cas9 turns off the gene’s signal completely – knocking it out. RNAi is also prone to off-target effects – disrupting unintended gene targets – while CRISPR-Cas9 showed more consistent results.

David Root, director of the Broad’s Genetic Perturbation Platform (formerly known as the RNAi Platform), and his platform colleagues assisted in the development of the GeCKO (genome-scale CRISPR knockout) screening technique reported in the Broad-McGovern study. In addition to RNAi screening, the platform now offers a range of genetic perturbation technologies to the Broad community. That list now includes the CRISPR-Cas9 system.

“The CRISPR-Cas9 screening method distinguishes itself from RNAi by producing knockouts instead of knockdowns and it will be cleaner for many phenotypes to see the complete knockout,” said Root who is a co-author of the Broad-McGovern paper. “The agreement among the distinct reagents targeting the same gene looks a lot higher for CRISPR-Cas9 compared to RNAi, which gives you a lot more confidence about gene specificity for these results.”

One of the unique advantages to the CRISPR-Cas9 system that researchers intend to explore in the future is that the system offers access to the world beyond genes: non-coding regions of the genome that may influence when and where proteins are produced in a manner that does not depend on their production of RNA. Such regions were out of reach for RNAi, but with CRISPR-Cas9, these elements may now be exploitable in mammalian cells.

“These papers together demonstrate the extraordinary power and versatility of the CRISPR-Cas9 system as a tool for genome-wide discovery of the mechanisms underlying mammalian biology,” said Eric Lander, director of the Broad Institute and co-senior author of one of the Science papers. “And we are just at the beginning: we’re still uncovering the capabilities of this system and its many applications.”

Other researchers who contributed to the Broad-Whitehead study include first author Tim Wang and Jenny J. Wei. Other researchers who contributed to the Broad-McGovern study include co-first authors Ophir Shalem and Neville Sanjana, Ella Hartenian, Xi Shi, David Scott, Tarjei Mikkelson, Benjamin Ebert, Dirk Heckl, and John Doench.

Funding for the former study was provided by the National Institutes of Health (NIH), National Human Genome Research Institute, the Broad Institute, and an award from the US National Science Foundation. The latter was supported by an NIH Director’s Pioneer Award, the NIH, the Keck Foundation, McKnight Foundation, Merkin Foundation, Vallee Foundation, Damon Runyon Foundation, Searle Scholars Foundation, Klingenstein Foundation, Simon Foundation, Klarman Family Foundation, Simons Center for the Social Brain at MIT, German Cancer Center, Bob Metcalfe, and Jane Pauley.

Paper(s) cited: 

Shalem, O* and Sanjana, N* et al. “Genome-scale CRISPR-Cas9 Knockout Screening in Human Cells.” Science DOI: 10.1126/science.1247005

Wang T. et al. “Genetic Screens in Human Cells Using the CRISPR/Cas9 System.” Science DOI: 10.1126/science.1246981

Hopes Dashed for HIV Cure with Bone Marrow Transplant

The announcement reveals hurdles to virus detection in patients

By Erika Check Hayden and Nature magazine

Two patients who researchers hoped had been cured of HIV have seen their infections return, dashing hopes that the virus had been eradicated from their bodies.

Scanning electron micrograph of HIV-1 virions budding from a cultured lymphocyte.Image: Public Health Image Library

The patients had received a treatment regimen similar to that given to Timothy Ray Brown, known as the "Berlin patient," who doctors said in 2009 had been cured of the virus by a bone-marrow transplant with cells that were resistant to HIV infection.

Unlike Brown, however, the two "Boston patients"—nicknamed for the Massachusetts city where they were treated—received bone-marrow transplants with cells that were not resistant to HIV. Still, both of them seemed to be free of the virus for months after stopping treatment with antiretroviral medications. But at a meeting on HIV persistence this week in Miami, Florida, researchers reported that the virus has rebounded in both of the Boston patients.

“It’s disappointing and very sobering,” says virologist Deborah Persaud of the Johns Hopkins Children's Center in Baltimore, Md., who reported in March that her team seemed to have cured an infant of HIV through treatment with antiretroviral medication.

Other researchers said that the news of the Boston patients was unfortunate, but not entirely unexpected, because they did not receive the same treatment as Brown.

Still, the result is very important for researchers seeking an HIV cure, says Steven Deeks, an HIV researcher and physician at the University of California, San Francisco. “The failure to cure these individuals will certainly influence the conduct of future clinical trials,” he says.

For instance, although the most powerful tests available indicated that the Boston patients were free of HIV after their transplants, it now seems that they were not. “It is now clear viral rebounds can happen at any time, even months after stopping therapy. People will have to followed very carefully for more prolonged periods than in the past,” Deeks says.

The Boston patients had received bone-marrow transplants to treat the blood cancer lymphoma—one underwent the procedure in 2008, the other in 2010. Both continued taking antiretroviral medications after the procedures. Eight months after each man’s transplant, researchers could detect no signs of HIV in his blood. This spring, both men elected to stop taking antiretroviral medications, and they both seemed to continue to remain free of HIV.

Their doctors, HIV specialists Timothy Henrich and Daniel Kuritzkes at Brigham and Women’s Hospital in Boston, announced at a meeting on July 3 that it was possible that the men had been cured.

But other researchers withheld judgement about whether the virus had been eliminated from the men’s bodies, given that the transplanted cells were not resistant to HIV infection.

Henrich and Kuritzkes thought that the men could have been cured by a phenomenon called graft-versus-host disease, a common complication of transplants, in which transplanted cells attack the body’s immune cells. The physicians speculated that this had eliminated all remaining HIV-infected cells.

When they made the announcement in July, Henrich and Kuritzkes said that it was too early to declare a cure, and only a month later, they were proved right. They detected HIV in one of the patients in August, 12 weeks after he had discontinued medication. The second patient kept his HIV in check longer, but the virus rebounded in November, 32 weeks after he had stopped medication.

Both men are now taking antiretroviral medications and are in good health, Henrich said on Dec. 6 in a statement. He says that the virus must have been hiding out somewhere in the men’s bodies, which will raise the bar for researchers trying to cure patients of HIV.

“Through this research we have discovered the HIV reservoir is deeper and more persistent than previously known and that our current standards of probing for HIV may not be sufficient to inform us if long-term HIV remission is possible if antiretroviral therapy is stopped,” Henrich said.

Both he and Deeks credited the men who participated in the research. “It is important to recognize the heroic sacrifices made by the study participants,” Deeks said. “The knowledge learned from their participation will shape the cure research agenda for years.”

Source: http://www.scientificamerican.com/article.cfm?id=hopes-dashed-for-hiv-cure&page=2

Researchers unlock a new means of growing intestinal stem cells

Studying these cells could lead to new treatments for diseases ranging from gastrointestinal disease to diabetes.

Anne Trafton, MIT News Office

Researchers at MIT and Brigham and Women’s Hospital have shown that they can grow unlimited quantities of intestinal stem cells, then stimulate them to develop into nearly pure populations of different types of mature intestinal cells. Using these cells, scientists could develop and test new drugs to treat diseases such as ulcerative colitis.

The small intestine, like most other body tissues, has a small store of immature adult stem cells that can differentiate into more mature, specialized cell types. Until now, there has been no good way to grow large numbers of these stem cells, because they only remain immature while in contact with a type of supportive cells called Paneth cells.

In a new study appearing in the Dec. 1 online edition of Nature Methods, the researchers found a way to replace Paneth cells with two small molecules that maintain stem cells and promote their proliferation. Stem cells grown in a lab dish containing these molecules can stay immature indefinitely; by adding other molecules, including inhibitors and activators, the researchers can control what types of cells they eventually become.

“This opens the door to doing all kinds of things, ranging from someday engineering a new gut for patients with intestinal diseases to doing drug screening for safety and efficacy. It’s really the first time this has been done,” says Robert Langer, the David H. Koch Institute Professor, a member of MIT’s Koch Institute for Integrative Cancer Research, and one of the paper’s senior authors.

Jeffrey Karp, an associate professor of medicine at Harvard Medical School and Brigham and Women’s Hospital, is also a senior author of the paper. The paper’s lead author is Xiaolei Yin, a postdoc at the Koch Institute and Brigham and Women’s Hospital.

From one cell, many

The inner layer of the intestines has several critical functions. Some cells are specialized to absorb nutrients from digested food, while others form a barrier that secretes mucus and prevents viruses and bacteria from entering cells. Still others alert the immune system when a foreign pathogen is present.

This layer, known as the intestinal epithelium, is coated with many small indentations known as crypts. At the bottom of each crypt is a small pool of epithelial stem cells, which constantly replenish the specialized cells of the intestinal epithelium, which only live for about five days. These stem cells can become any type of intestinal epithelial cell, but don’t have the pluripotency of embryonic stem cells, which can become any cell type in the body.

If scientists could obtain large quantities of intestinal epithelial stem cells, they could be used to help treat gastrointestinal disorders that damage the epithelial layer. Recent studies in animals have shown that intestinal stem cells delivered to the gut can attach to ulcers and help regenerate healthy tissue, offering a potential new way to treat ulcerative colitis.

Using those stem cells to produce large populations of specialized cells would also be useful for drug development and testing, the researchers say. With large quantities of goblet cells, which help control the immune response to proteins found in food, scientists could study food allergies; with enteroendocrine cells, which release hunger hormones, they could test new treatments for obesity. 

“If we had ways of performing high-throughput screens on large numbers of these very specific cell types, we could potentially identify new targets and develop completely new drugs for diseases ranging from inflammatory bowel disease to diabetes,” Karp says.

Controlling cell fate

In 2007, Hans Clevers, a professor at the Hubrecht Institute in the Netherlands, identified a marker for intestinal epithelial stem cells — a protein called Lgr5. Clevers, who is an author of the new Nature Methods paper, also identified growth factors that enable these stem cells to reproduce in small quantities in a lab dish and spontaneously differentiate into mature cells, forming small structures called organoids that mimic the natural architecture of the intestinal lining.

In the new study, the researchers wanted to figure out how to keep stem cells proliferating but stop them from differentiating, creating a nearly pure population of stem cells. This has been difficult to do because stem cells start to differentiate as soon as they lose contact with a Paneth cell.

Paneth cells control two signaling pathways, known as Notch and Wnt, which coordinate cell proliferation, especially during embryonic development. The researchers identified two small molecules, valproic acid and CHIR-99021, that work together to induce stem cells to proliferate and prevent them from differentiating into mature cells.

When the researchers grew mouse intestinal stem cells in a dish containing these two small molecules, they obtained large clusters made of 70 to 90 percent stem cells.

Once the researchers had nearly pure populations of stem cells, they showed that they could drive them to develop into particular types of intestinal cells by adding other factors that influence the Wnt and Notch pathways. “We used different combinations of inhibitors and activators to drive stem cells to differentiate into specific populations of mature cells,” Yin says.

This approach also works in mouse stomach and colon cells, the researchers found. They also showed that the small molecules improved the proliferation of human intestinal stem cells. They are now working on engineering intestinal tissues for patient transplant and developing new ways to rapidly test the effects of drugs on intestinal cells.

Another potential use for these cells is studying the biology that underlies stem cells’ special ability to self-renew and to develop into other cell types, says Ramesh Shivdasani, an associate professor of medicine at Harvard Medical School and Dana-Farber Cancer Institute.

“There are a lot of things we don’t know about stem cells,” says Shivdasani, who was not part of the research team. “Without access to large quantities of these cells, it’s very difficult to do any experiments. This opens the door to a systematic, incisive, reliable way of interrogating intestinal stem cell biology.”

The research was funded by the National Institutes of Health, a Harvard Institute of Translational Immunology/Helmsley Trust Pilot Grant in Crohn’s Disease, and the European Molecular Biology Organization.


Source: MIT.edu

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Exclusive: 'Jaw-dropping' breakthrough hailed as landmark in fight against hereditary diseases as Crispr technique heralds genetic revolution

Development to revolutionise study and treatment of a range of diseases from cancer, incurable viruses such as HIV to inherited genetic disorders such as sickle-cell anaemia and Huntington’s disease

A breakthrough in genetics – described as “jaw-dropping” by one Nobel scientist – has created intense excitement among DNA experts around the world who believe the discovery will transform their ability to edit the genomes of all living organisms, including humans.

The development has been hailed as a milestone in medical science because it promises to revolutionise the study and treatment of a range of diseases, from cancer and incurable viruses to inherited genetic disorders such as sickle-cell anaemia and Down syndrome.

For the first time, scientists are able to engineer any part of the human genome with extreme precision using a revolutionary new technique called Crispr, which has been likened to editing the individual letters on any chosen page of an encyclopedia without creating spelling mistakes. The landmark development means it is now possible to make the most accurate and detailed alterations to any specific position on the DNA of the 23 pairs of human chromosomes without introducing unintended mutations or flaws, scientists said.

The technique is so accurate that scientists believe it will soon be used in gene-therapy trials on humans to treat incurable viruses such as HIV or currently untreatable genetic disorders such as Huntington’s disease. It might also be used controversially to correct gene defects in human IVF embryos, scientists said.

Until now, gene therapy has had largely to rely on highly inaccurate methods of editing the genome, often involving modified viruses that insert DNA at random into the genome – considered too risky for many patients.

The new method, however, transforms genetic engineering because it is simple and easy to edit any desired part of the DNA molecule, right down to the individual chemical building-blocks or nucleotides that make up the genetic alphabet, researchers said.

“Crispr is absolutely huge. It’s incredibly powerful and it has many applications, from agriculture to potential gene therapy in humans,” said Craig Mello of the University of Massachusetts Medical School, who shared the 2006 Nobel Prize for medicine for a previous genetic discovery called RNA interference.

“This is really a triumph of basic science and in many ways it’s better than RNA interference. It’s a tremendous breakthrough with huge implications for molecular genetics. It’s a real game-changer,” Professor Mello toldThe Independent.

“It’s one of those things that you have to see to believe. I read the scientific papers like everyone else but when I saw it working in my own lab, my jaw dropped. A total novice in my lab got it to work,” Professor Mello said.

In addition to engineering the genes of plants and animals, which could accelerate the development of GM crops and livestock, the Crispr technique dramatically “lowers the threshold” for carrying out “germline” gene therapy on human IVF embryos, Professor Mello added.

Germline gene therapy on sperm, eggs or embryos to eliminate inherited diseases alters the DNA of all subsequent generations, but fears over its safety, and the prospect of so-called “designer babies”, has led to it being made illegal in Britain and many other countries.

The new gene-editing technique could address many of the safety concerns because it is so accurate. Some scientists now believe it is only a matter of time before IVF doctors suggest that it could be used to eliminate genetic diseases from affected families by changing an embryo’s DNA before implanting it into the womb.

“If this new technique succeeds in allowing perfectly targeted correction of abnormal genes, eliminating safety concerns, then the exciting prospect is that treatments could be developed and applied to the germline, ridding families and all their descendants of devastating inherited disorders,” said Dagan Wells, an IVF scientist at Oxford University.

“It would be difficult to argue against using it if it can be shown to be as safe, reliable and effective as it appears to be. Who would condemn a child to terrible suffering and perhaps an early death when a therapy exists, capable of repairing the problem?” Dr Wells said.

The Crispr process was first identified as a natural immune defence used by bacteria against invading viruses. Last year, however, scientists led by Jennifer Doudna at the University of California, Berkeley, published a seminal study showing that Crispr can be used to target any region of a genome with extreme precision with the aid of a DNA-cutting enzyme called CAS9.

Since then, several teams of scientists showed that the Crispr-CAS9 system used by Professor Doudna could be adapted to work on a range of life forms, from plants and nematode worms to fruit flies and laboratory mice.

Earlier this year, several teams of scientists demonstrated that it can also be used accurately to engineer the DNA of mouse embryos and even human stem cells grown in culture. Geneticists were astounded by how easy, accurate and effective it is at altering the genetic code of any life form – and they immediately realised the therapeutic potential for medicine.

“The efficiency and ease of use is completely unprecedented. I’m jumping out of my skin with excitement,” said George Church, a geneticist at Harvard University who led one of the teams that used Crispr to edit the human genome for the first time.

“The new technology should permit alterations of serious genetic disorders. This could be done, in principle, at any stage of development from sperm and egg cells and IVF embryos up to the irreversible stages of the disease,” Professor Church said.

David Adams, a DNA scientist at the Wellcome Trust Sanger Institute in Cambridge, said that the technique has the potential to transform the way scientists are able to manipulate the genes of all living organisms, especially patients with inherited diseases, cancer or lifelong HIV infection.

“This is the first time we’ve been able to edit the genome efficiently and precisely and at a scale that means individual patient mutations can be corrected,” Dr Adams said.

“There have been other technologies for editing the genome but they all leave a ‘scar’ behind or foreign DNA in the genome. This leaves no scars behind and you can change the individual nucleotides of DNA – the ‘letters’ of the genetic textbook – without any other unwanted changes,” he said.

Timeline: Landmarks in DNA science

Restriction enzymes: allowed scientists to cut the DNA molecule at or near a recognised genetic sequence. The enzymes work well in microbes but are more difficult to target in the more complex genomes of plants and animals. Their discovery in the 1970s opened the way for the age of genetic engineering, from GM crops to GM animals, and led to the 1978 Nobel Prize for medicine.

Polymerase chain reaction (PCR): a technique developed in 1983 by Kary Mullis (below, credit: Getty) in California allowed scientists to amplify the smallest amounts of DNA – down to a single molecule – to virtually unlimited quantities. It quickly became a standard technique, especially in forensic science, where it is used routinely in analysing the smallest tissue samples left at crime scenes. Many historical crimes have since been solved with the help of the PCR test. Mullis won the Nobel Prize for chemistry in 1993.

RNA interference: scientists working on the changing colour of petunia plants first noticed this phenomenon, which was later shown to involve RNA, a molecular cousin to DNA. In 1998, Craig Mello and Andrew Fire in the US demonstrated the phenomenon on nematode worms, showing that small strands of RNA could be used to turn down the activity of genes, rather like a dimmer switch. They shared the 2006 Nobel Prize for physiology or medicine for the discovery.

Zinc fingers: complex proteins called zinc fingers, first used on mice in 1994, can cut DNA at selected sites in the genome, with the help of enzymes. Another DNA-cutting technique called Talens can do something similar. But both are cumbersome to use and difficult to operate in practice – unlike the Crispr technique.

Click HERE to see a video of how the Crispr system derived from bacteria works on human cells to correct genetic defects