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survivor, and patient advocate who consults for TAPUR and was involved in the
I-SPY2 study, among other trials.) “It
will be less rigorous than other trials
but more generalizable,” she said. The
regulatory pathway to gaining approval
for new indications from the TAPUR
study will need to be worked out with
the U.S. Food and Drug Administration,
Perlmutter said.
One hallmark of TAPUR is its inclusiveness. It will accept a broader patient
population than typical clinical trials,
such as patients with a lower performance status than those eligible for
MATCH and other trials, who will generally have other trial options available
to them. “Patients in TAPUR will have
malignancies that have progressed after
at least one or two lines of standard
chemotherapy, who have already undergone genomic testing by a commercially
available platform, and who are running
out of options,” Loaiza-Bonilla said.
“TAPUR is ideal for a patient that for
whom the off-label targeted drug has
been difficult due to high copay, ineligibility for clinical trial, or insurance
denial,” Loaiza-Bonilla said. One major
difference between MATCH and TAPUR
is that MATCH will have more drugs
available to patients, both approved and
investigational.
With a decentralized design, TAPUR
will enable a patient’s own oncologist
to send tumor biopsy samples to be
sequenced to a local CLIA-certified lab,
and the physician will select a drug to
test on the basis of the tumor’s genomic
profile. “An advantage to TAPUR is that
we can use the information from several genomics platforms and do not
need a fresh biopsy [sample] for eligibility,” Loaiza-Bonilla said. If a drug–target
match is not made, the oncologist can
consult a molecular tumor board, which
will review the genomic and clinical
aspects of the case and suggest potential
therapies either in or off the study, he
said. As with any clinical trial, all patients
in the TAPUR study will be monitored for
efficacy, including tumor response, progression-free survival, overall survival,
and side effects.
Although patients will receive the
drugs for free, ASCO expects that patients’
insurance will cover their care, including routine blood tests, antibiotics, and
hospitalizations. ASCO did not, however,
describe agreements with insurers. Three
committees will oversee TAPUR, each of
which will include investigators, genomics experts, and patient representatives.
A steering committee will oversee study
operations, develop data sharing and publication policies, review plans to add or
remove drugs from a study, and approve
additional study sites. The molecular
tumor board will review proposed drug–
target matches and discuss with physicians possible treatments, on or off study.
The data and safety monitoring board will
review results independently to analyze
and monitor side effects.
Some physicians, such as LoaizaBonilla, will have some patients who participate in TAPUR and others in MATCH.
Oncologists will need to decide which trial
is best suited for their patients, he said.
“The two studies are completely different and complement each other,”
he said. “TAPUR will enable patients
to get off-label [targeted] therapies for
free, which may or may not work, without leaving their [physician’s medical] practice,” Perlmutter said. TAPUR
patients will not need new biopsies,
whereas MATCH patients will. MATCH
will have more scientific rigor. TAPUR’s
tumor biopsy samples will be processed by any CLIA-certified lab available to clinicians. For MATCH, however,
fresh biopsy samples will be required
and processed in the same way, at one
of four sites. So the data gleaned from
that trial will be “more like comparing
apples to apples,” Loaiza-Bonilla said.
Another difference is that with TAPUR,
the patient’s physician will choose the
treatment, whereas for MATCH the
primary investigator for each arm will
choose the treatment in consultation
with the patient’s doctor.
“At the crux, TAPUR will collect data,
whereas MATCH is a collection of phase
II trials meant to find an endpoint,
not just observe what happens,” said
Barbara Conley, M.D., co–primary investigator of MATCH and associate director
of the Cancer Diagnosis Program in the
division of cancer treatment and diagnosis at the National Cancer Institute.
“If a trial in MATCH meets predesignated endpoints, we have some flexibility, and that trial will be expanded,”
she said. Alice P. Chen, M.D., acting head
of the Early Clinical Trials Development
Program in the same NCI division, noted
that treatment selection in MATCH is
being done in a strictly “rule based,”
computerized process, in contrast to
TAPUR. In MATCH, an opportunity to
rebiopsy and resequence samples from
patients who relapse will be available,
whereas it is unclear whether patients
who relapse in TAPUR will be offered
new treatments—and on what basis if
new biopsies are not done.
“While TAPUR is not the be-all and
end-all [of clinical trials], it’s a step in
the right direction,” Perlmutter said. The
more opportunities there are to learn
from, and the more patients who can get
targeted treatments, the better, she said.
© Oxford University Press 2015.
DOI:10.1093/jnci/djv356
First published online November 4, 2015
Scientists Journey Into Genomes Via CRISPR-Cas9
By Delthia Ricks
Cancer researchers are testing an evolving gene-editing technology that lets
them manipulate DNA. Cold Spring
Harbor Laboratory (CSHL) in New York
is one of dozens of institutions using
the
technique—clustered
regularly
interspaced short palindromic repeats
(CRISPR)–Cas9—to investigate genomes.
The revolutionary technology has
drawn a spotlight in and out of cancer
research because of the simplicity, precision, and speed with which researchers
can manipulate the basic chemical components of life. But even as this potent
form of gene editing has stirred the
research community with its promise,
the technology is coming under scrutiny. A group of influential scientists
convened in California earlier this year
to discuss ethical concerns that CRISPR–
Cas9 raised and called for a moratorium
on using it in germline research.
Investigators at CSHL, however,
along with a growing number of cancer
researchers worldwide, are hailing the
technology a boon to biomedical science.
Researchers cite the unprecedented ease
with which they can use this technology
to write and edit in the alphabet of life.
“CRISPR–Cas9 is a powerful tool that
allows us to change the letters of the
DNA code, particularly in experimental systems like model organisms and
mouse models,” said Christopher Vakoc,
M.D., Ph.D., lead investigator of CSHL’s
research. The emerging method of
knocking in or knocking out sequences
has allowed him and his team to embark
on sweeping genomic hunts in search of
new targets for drugs.
Vakoc and his CSHL collaborators
are using CRISPR–Cas9 genomic engineering technology to mount genomic
expeditions across cancers of the blood,
pancreas, colon, liver, lungs and muscles. “By changing the letters of the DNA
code, you can actually reveal in a matter of weeks all potential drug targets—
every little pocket of opportunity—that a
cancer uses.
“We can draw bulls-eyes around
these pockets for drug discovery,” Vakoc
said, noting the drug targets that he and
his colleagues have uncloaked provide
tangible sites for current and future cancer drug research.
Still only a year into their CRISPRbased hunts, Vakoc and his team have
uncovered 19 binding domains in acute
myelogenous leukemia that are new to
science and critical to the cancer’s persistence. The technology allowed the
researchers to make the sweeping discoveries in one experiment.
In use only since 2012, the gene-editing system relies on a bacterial enzyme,
Cas9, that cleanly cuts double-stranded
DNA at loci specified by a single-guide
RNA. Different sequences can be encoded
into the guide strand, which enables scientists to cut and paste at will.
Feng
Zhang,
Ph.D.,
of
the
Massachusetts Institute of Technology
(MIT) in Cambridge, collaborating with
colleagues at MIT’s Broad Institute and
its David H. Koch Institute for Integrative
Cancer Research, used CRISPR–Cas9 to
systematically turn off all genes across
the genome in an animal model of cancer. The research, reported in a March
issue of the biweekly journal Cell, uncovered sequences involved in tumor evolution and metastasis.
“We have been working with CRISPR
for several years now and developed a
[unique] system for using CRISPR with
eukaryotic cells,” said Zhang, a leading
developer of the technology. “You can
use CRISPR–Cas9 to study a small number of genes or a large numbers of genes,”
Zhang said. “In terms of cancer you can
knock in or knock out certain genes, and
the advantage of it is the speed with
which you can do it.”
Nobel Prize–winning biologist David
Baltimore, Ph.D., is president emeritus
of the California Institute of Technology
“You can use CRISPR–Cas9
to study a small number of
genes or a large numbers
of genes. In terms of
cancer you can knock in or
knock out certain genes,
and the advantage of it is
the speed with which you
can do it.”
and holder of the Robert Andrews
Millikan chair in biology. He said that he
sees cancer research as an area where
CRISPR–Cas9 will flourish. “There are in
my mind no technical problems or moral
issues,” he said, adding that the technology is an ideal tool to use in developing
animal models.
The problem with CRISPR–Cas9 compared with other forms of DNA editing,
Baltimore said, is the potential for germline modification. In April, researchers in China reported an attempt to
genetically modify 86 human embryos
carrying a β-thalassemia mutation.
Although the scientists said they were
unsuccessful, another group of investigators in China last year produced
two infant monkeys via CRISPR–Cas9.
“Until CRISPR came along it was difficult doing gene modification in the
human genome. CRISPR changed everything. Now there is a way to modify the
genome to affect future generations,”
Baltimore added.
He and 16 other scientists, including
CRISPR’s codeveloper Jennifer Doudna,
Ph.D., professor of biochemistry and
molecular biology at the University of
California, Berkeley, met earlier this year
in Napa, Calif., to discuss the ethics of
the technology. They called for the moratorium because of the potential for mischief in the wrong hands.
Vakoc’s investigations, meanwhile,
are among increasing research efforts to
use the technology to seek therapeutic
targets. Pharmaceutical giant Novartis
announced last winter that it also would
pursue CRISPR-based research. Novartis
officials described a collaborative agreement with Intellia Therapeutics in
Cambridge, Mass., and a licensing pact
with Caribou Biosciences in Berkeley,
Calif., founded by Doudna. The deal
with Caribou involves developing drug
discovery tools, Novartis officials said.
Through the collaborative agreement with Intellia, investigators plan
to engineer chimeric antigen receptor T
cells and hematopoietic stem cells. The
former will be designed to seek out specific sites on cancer cells and disable
them. If successful, the pursuit could
result in a new
and highly targeted therapy.
Although
only 3 years
old, the geneediting technology borrows on
a genomic process dating back
e o n s . C R I S P R
RNAs and assoFeng Zhang, Ph.D.
ciated Cas proteins make up the the acquired immune
system of bacteria and archaea.
As early as the 1980s, scientists in Japan
observed alternating clusters of Escherichia
coli DNA interspersed with viral spacer
sequences in a mosaic arrayed throughout
the microbe’s chromosomal loop.
Yet, it was not until 8 years ago that
microbiologists confirmed the phenomenon as part of a sophisticated acquired
immune system common to bacteria and
archaea. These microbes recognize infiltrators infecting the cell from genetic
information stored in spacer sequences.
The immune pathway for these species
is therefore characterized by clustered,
regularly interspaced, short palindromic
repeat (CRISPR) sequences.
Jacob Corn, Ph.D., managing director
and scientific director of the Innovative
Genomic Initiative in Berkeley, Calif.,
calls CRISPR–Cas9 a groundbreaking
development. He and likens it to other
advances in biology, such as the discovery of DNA’s helical structure and the
development of PCR. Moreover, it is so
simple to use that undergraduates master CRISPR in only days, Corn said.
CRISPR’s workhorse is an enzyme
called Cas—shorthand for “CRISPRassociated,” Corn added. Cas9 was isolated from Streptococcus pyogenes and is
specific to that bacterium. In microbial
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NEWS | 5 of 8
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cells under siege, Cas is deployed against
invaders, usually bacteriophages. A Cas
enzyme is a masterly gene-cutting engine.
It uses two bound RNAs—guide and
tracer strands—that are central to their
activity. Cas innately interacts with DNA
and generates clean double-stranded
breaks at loci specified by the guide RNA.
In June 2012, Doudna and Emmanuelle
Charpentier, a microbiologist at Umea
University in Sweden, set the scientific
community astir when they reported in
the journal Science how they transformed
the bacterial defense strategy into a new
way to modify genes by hand. A member
of Doudna’s team also figured out how to
combine the activity of two of nature’s
CRISPR RNAs into a single-guide strand.
Doudna received the 2014 Lurie Prize
in Biomedical Sciences awarded by the
Foundation for the National Institutes
of Health. Last fall, she and Charpentier
each won a $3 million Breakthrough
Prize for their CRISPR research. The
honor was funded by several big names
in technology,including the founders of
Facebook, Google, and the DNA company
23andMe.
Other
gene-modifying
technologies have never generated the excitement surrounding CRISPR. Zinc finger
nucleases can achieve double-stranded
DNA breaks, as can transcription activator–like effector nucleases. But some
biologists have complained that both
types of nucleases can be finicky. Neither
possesses the reliability or simplicity of
CRISPR–Cas9, said MIT’s Zhang.
His institution holds the only U.S. patent on CRISPR–Cas9 technology. The
University of California and the Broad
Institute of MIT and Harvard University
are embroiled in an intellectual property
dispute over which was first to develop
the gene-editing system. Zhang insists
the method emerged in his laboratory, not
Doudna’s. Corn said there is no question
that Doudna and Charpentier were first.
Vakoc credits his graduate student,
Junwei Shi, as the catalyst behind his
lab’s move to CRISPR–Cas9 last year.
Their research allowed them to “rediscover” six key targets already known
in acute myelogenous leukemia. With
CRISPR–Cas9 it took about 2 weeks to
uncover what had taken scientists using
conventional methods 60 years to find.
Vakoc won the prestigious Outstanding
Achievement in Cancer Research Award
from the American Association for
Cancer Research earlier this year. He and
other investigators marvel at how quickly
they now produce mouse models.
“Mouse models can be made very
quickly with this technology, so for cancer research CRISPR is really transformative,” Corn said. . “In a variety of cancers
there are all kinds of passenger mutations. But there are also driver mutations
and you may want to show how they
proliferate. With genome editing you
can very rapidly test mutations and ask
whether they are a cause of the cancer,”
said Corn, a former cancer researcher at
Genentech.
He said the work under way at CSHL
by Vakoc and colleagues is important
because it shows how CRISPR–Cas9 helps
produce answers expeditiously when
investigating the genome.
© Oxford University Press 2015.
DOI:10.1093/jnci/djv352
First published online November 4, 2015
Targeted Therapy Makes Inroads in Medulloblastoma
By Charlie Schmidt
Children with medulloblastoma, a rare
brain cancer, face a challenging prognosis.
Standard treatments have boosted 5-year
survival rates beyond 80%, but depending
on a child’s age, side effects—especially
from radiation to the brain and spinal
cord—can be devastating. Younger children, with their rapidly developing nervous
systems, can wind up with substantial cognitive deficits that make it difficult for them
to live independently as adults. Scientists
are therefore highly motivated to develop
more targeted therapies that could limit
the need for radiation—or at least delay it
until a child becomes old enough to tolerate treatment without a major drop in IQ.
Last July, investigators reported considerable progress toward that goal. In
two concurrent phase II clinical trials,
treatment with a targeted drug called
vismodegib, which is approved already
for basal cell carcinomas of the skin,
shrank or eliminated tumors in four
of 43 treated patients for 2 months or
more. And in 13 patients, vismodegib
stopped tumor growth for 17 months.
The study was published in the Journal
of Clinical Oncology. Vismodegib targets
smoothened, a protein with key roles
in the sonic hedgehog (SHH) signaling
pathway that regulates organogenesis
and neurodevelopment. About a third of
all medulloblastoma patients have SHHdriven disease, meaning the pathway
is hyperactivated to the degree that it
drives abnormal cell growth. Lead study
author Giles Robinson, M.D., is a pediatric neurooncologist at St. Jude Children’s
Research Hospital in Memphis, Tenn.
He said that as expected, vismodegib
worked only in the SHH patients and not
in others with medulloblastoma caused
by other genetic defects. “Not all the SHH
cancers responded to smoothened inhibition, and that shows we still need to be
more specific with our targets,” he said.
Insights From Gorlin
Syndrome
Medulloblastoma afflicts roughly 500
patients annually in the United States.
Once viewed as a single tumor entity, it’s
now regarded as four illnesses, “as distinct from one another as breast cancer
is from colon cancer,” said Yoon-Jae Cho,
M.D., assistant professor of neurology
and neurosurgery at Stanford University
Palo Alto, Calif. Besides SHH, patients can
fall into one of three other subgroups:
the WNT subgroup, which has the best
prognosis; the Group 3 subgroup, which
has the worst; and the Group 4 subgroup, which is the most common type
of medulloblastoma, accounting for
roughly 40% of all cases.
The idea to test vismodegib in the
SHH subgroup was based on the cancer’s shared biology with Gorlin syndrome. Patients with that condition
develop basal cell carcinomas throughout the body and are at high risk for SHH
medulloblastoma. Gorlin syndrome typically results from inherited mutations
in a gene that codes for PTCH1, a transmembrane protein in the SHH pathway.
A tumor suppressor, PTCH1 normally
prevents smoothened from becoming