Powerful New Way To Edit DNA: Must read Xenogenesis to see the end game. Human species wipeout!
March 5, 2014-In
the late 1980s, scientists at Osaka University in Japan noticed unusual
repeated DNA sequences next to a gene they were studying in a common
bacterium. They mentioned them in the final paragraph of a paper:
“The biological significance of these sequences is not known.” Now
their significance is known, and it has set off a scientific frenzy.
The
sequences, it turns out, are part of a sophisticated immune system that
bacteria use to fight viruses. And that system, whose very existence
was unknown until about seven years ago, may provide scientists with
unprecedented power to rewrite the code of life.
In
the past year or so, researchers have discovered that the bacterial
system can be harnessed to make precise changes to the DNA of humans, as
well as other animals and plants.
This
means a genome can be edited, much as a writer might change words or
fix spelling errors. It allows “customizing the genome of any cell or
any species at will,” said Charles Gersbach, an assistant professor of biomedical engineering at Duke University.
Already the molecular system, known as Crispr,
is being used to make genetically engineered laboratory animals more
easily than could be done before, with changes in multiple genes.
Scientists in China recently made monkeyswith changes in two genes.
Scientists
hope Crispr might also be used for genomic surgery, as it were, to
correct errant genes that cause disease. Working in a laboratory — not,
as yet, in actual humans — researchers at the Hubrecht Institute in the Netherlands showed they could fix a mutation that causescystic fibrosis.
But
even as it is stirring excitement, Crispr is raising profound
questions. Like other technologies that once wowed scientists — like
gene therapy, stem cells and RNA interference — it will undoubtedly encounter setbacks before it can be used to help patients.
It
is already known, for instance, that Crispr can sometimes change genes
other than the intended ones. That could lead to unwanted side effects.
The
technique is also raising ethical issues. The ease of creating
genetically altered monkeys and rodents could lead to more animal
experimentation. And the technique of altering genes in their embryos
could conceivably work with human embryos as well, raising the specter
of so-called designer babies.
“It does make it easier to genetically engineer the humangerm line,” said Craig C. Mello,
a Nobel laureate at the University of Massachusetts Medical School,
referring to making genetic changes that could be passed to future
generations.
Still,
Crispr is moving toward commercial use. Five academic experts recently
raised $43 million to start Editas Medicine, a company in Cambridge,
Mass., that aims to treat inherited disease. Other start-ups include
Crispr Therapeutics, which is being formed in London, and Caribou
Biosciences in Berkeley, Calif.
Agricultural
companies might use Crispr to change existing genes in crops to create
new traits. That might sidestep the regulations and controversy
surrounding genetically engineered crops, which generally have foreign DNA added.
The
development of the new tool is an example of the unanticipated benefits
of basic research. About 15 years ago, after it became possible to
sequence the entire genomes of bacteria, scientists noticed that many
species had those repeated DNA sequences that were first noticed a
decade earlier in Osaka. They were called “clustered regularly
interspaced short palindromic repeats” — Crispr for short.
Breaking the Chain
A complex immune system found in bacteria is already proving useful in editing DNA and may lead to future therapies.
STORAGE Researchers in the 1980s noticed that bacteria had small
blocks of palindromic DNA repeated many times, with nonrepeated spacers
of DNA stored in between. This pattern is a sophisticated immune system
known by the acronym Crispr, for “clustered regularly interspaced short
palindromic repeats.”
RECOGNITION These spacers match pieces of DNA from viral invaders
that bacteria or their ancestors have faced before. When needed, the DNA
contained in the spacer is converted to RNA. An enzyme and a second
piece of RNA latch on, forming a structure that will bind to strands of
DNA that match the spacer’s sequence.
CUTTING When a matching strand of DNA is found, the enzyme opens the
double helix and cuts both sides. The double cut breaks the strand and
disables the viral DNA. If a bacterium survives an attack by an
unfamiliar virus, it will make and store a new spacer, which can be
inherited by future generations.
EDITING Researchers are learning how to use synthetic RNA sequences
to control the cutting of any piece of DNA they choose. The cell will
repair the cut, but an imperfect repair may disable the gene. Or a
snippet of different DNA can be inserted to fill the gap, effectively
editing the DNA sequence.
By The New York Times
Sources: Nature; Addgene
But
what was their purpose? In 2007, researchers at Danisco, a company that
supplies bacterial cultures used in making cheese and yogurt, confirmed hypotheses that Crispr protects bacteria from viruses.
It
is part of an adaptive immune system — one that remembers a pathogen so
it is ready the next time that same invader appears. The human adaptive
immune system is why people get measles only once and why vaccines work. But it was not imagined that single-cell organisms like bacteria had such systems.
Here
is how it works. The repeated DNA sequences in the bacterial genome are
separated from one another by other sequences. These “spacers” are
excerpts from the sequences of viruses that have attacked the bacterium
or its ancestors. They are like genetic mug shots, telling the bacterium
which bad guys to watch for. The Crispr defense system will slice up
any DNA with that same sequence, so if the same virus invades again, it
will be destroyed.
If a previously unseen virus attacks, a new spacer, a new mug shot, is made and put at the end of the chain.
That means the Crispr region “is like a tape recording of exposure to prior invaders,” said Erik J. Sontheimer, a Northwestern University professor who helped unravel the mechanism.
And
it provides a way to tell two bacterial strains apart, because even two
strains from the same species are likely to have encountered different
viruses. This is already being used to identify sources of
food-poisoning outbreaks.
Cheese
and yogurt companies can examine Crispr regions to see if their
bacterial cultures are immunized against particular viruses that could
slow production.
“Now you can extend the shelf life of that great strain,” saidRodolphe Barrangou of
North Carolina State University, who previously worked at Danisco and
was the lead author on the 2007 paper. “That has changed the game quite a
bit for the dairy industry.”
The real frenzy, however, started in 2012, when a team led by Emmanuelle Charpentier, then at Umea University in Sweden, and Jennifer A. Doudna of the University of California, Berkeley, demonstrated a way for researchers to use Crispr to slice up any DNA sequence they choose.
We’re still learning new and fascinating things about a class of
fossils, long gone but not short on character; a new technique allows a
kind of chromosomal editing; Neil deGrasse Tyson talks about hosting the
new-old series “Cosmos.”
By DAVID CORCORAN and JEFFERY DelVISCIO
Scientists
must synthesize a strand of DNA’s chemical cousin RNA, part of which
matches the DNA sequence to be sliced. This “guide RNA” is attached to a
bacterial enzyme called Cas9. When the guide RNA binds to the
corresponding DNA sequence, Cas9 cuts the DNA at that site.
The
cell tries to repair the cut but often does so imperfectly, which is
enough to disable, or knock out a gene. To change a gene, scientists
usually insert a patch — a bit of DNA similar to where the break
occurred but containing the desired change. That patch is sometimes
incorporated into the DNA when the cell repairs the break.
Would
this work in organisms besides bacteria? “I knew it was like firing a
starting gun in a race,” Dr. Doudna said, but sure enough, by early 2013
scientists had shown it would work in human cells, and those of many
other animals and plants, even though these species are not known to
have Crispr-based immune systems.
“I don’t know any species of plant or animal where it has been tried and it failed,” said George Church, a professor ofgenetics at Harvard Medical School. “It allows you to do genome engineering on organisms that are very hard to do otherwise.”
In
the past, making an animal with multiple genetic changes usually
required creating separate animals with single changes and then
crossbreeding them to produce offspring with multiple changes. With
Crispr, multiple genetic changes can be made in one step, by putting
multiple guide RNAs into the cell.
“It
just completely changes the landscape,” Dr. Doudna said. Berkeley
scientists used to farm out that work to specialized laboratories or
companies. Now, she said, “people are able to make mice in their own
labs.”
There are other techniques that can do what Crispr does, though Crispr is “the easiest by far,” Dr. Church said.
RNA
interference, for instance, can silence particular genes. It is similar
to Crispr in that it also uses RNA that matches the gene to be
silenced.
But
RNA interference works by inhibiting messenger RNA, which translates a
gene into a protein. That usually provides only a partial and temporary
disabling of the gene, because the cell can make new messenger RNA.
Crispr disables the gene itself, potentially a more complete and
permanent inactivation.
There are also already ways to change genes, namely zinc-finger nucleases and
transcription activator-like effector nucleases, or Talens. The
biotechnology company Sangamo BioSciences is already conducting a
clinical trial of a treatment for H.I.V. that uses zinc fingers to alter patients’ immune cells to make them resistant to the virus.
Both
techniques use proteins to guide where the DNA is cut; it is more
difficult to develop a protein that binds to a specific DNA sequence
than it is to make a piece of RNA with the matching sequence.
With
zinc fingers “it might take you months or years to get something to
work well for one gene,” said Dr. Gersbach at Duke. With Crispr, “it
takes days to weeks.”
Quick
is not always accurate, however. While Crispr is generally precise, it
can have off-target effects, cutting DNA at places where the sequence is
similar but not identical to that of the guide RNA.
Crispr “may not yet have adequate specificity to completely displace” the older techniques, Dana Carroll, a biochemistry professor at the University of Utah, wrote in a commentaryin Nature Biotechnology in September.
Still, scientists are already figuring out how to make Crispr more specific.
Another obstacle for treating diseases will be the delivery of the genetic changes to all the cells in the body that need it.
For
some diseases, it may be possible to extract blood stem cells from the
body, alter them using Crispr, and put them back. If that is not
possible, the DNA needed to make Cas9, the guide RNA and the corrective
patch might be put into a disabled virus. This technique is used for
gene therapy, but does not always work well.
It is likely to be a few years before Crispr is tested in people. For now, there is a lot more to learn about it.
Chase L. Beisel at North Carolina State reported that
Crispr could be used to kill one strain of bacteria in a mixture of
strains, by targeting a sequence unique to that strain. That might one
day lead to antibiotics that can kill the bad bugs without also killing the good ones.
David S. Weiss of Emory University found that some bacteria use
Cas9 to silence one of their own genes, rather than that of a virus, to
help them evade detection by their host’s immune system.
The
pace of new discoveries and applications is dizzying. “All of this has
basically happened in a year,” Dr. Weiss said. “It’s incredible
No comments:
Post a Comment