Protein Turnover Provides Pancreatic Cancer Target€¦ · mutations but artifacts of the sonica-tion process. Laurence Ettwiller, PhD, and her colleagues from New England Biolabs
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NEWS IN BRIEF
APRIL 2017�CANCER DISCOVERY | 345
that errors introduced during library
construction can be detected among
duplicate sequences and remedied
computationally. “I like molecular bar-
coding because you’re able to directly
measure the type and degree of DNA
damage,” Pugh says. “You’re reading
out exactly what you have in the tube
and then correcting for it.”
However, repairing DNA was not the
study’s primary aim. “The goal of the
paper was to alert the community to a
potential problem,” says Tom Evans,
PhD, an enzymologist at NEB. “Solu-
tions will come later.” –Elie Dolgin ■
Protein Turnover Provides Pancreatic Cancer Target
Pancreatic adenocarcinoma is such an
aggressive and deadly cancer that fewer
than 1 in 3 patients live long enough
to see the one-year anniversary of their
diagnosis. For the majority of patients,
surgery is not an option and their
tumors have evolved to the point that
they’re not responsive to chemotherapy.
Finding new drugs for pancreatic
cancer has proven elusive. But accord-
ing to new research, one of the mol-
ecular adaptations that makes these
cells more aggressive and treatment-
resistant also presents a vulnerability
that can be exploited for therapeutic
purposes (Nature 2017;542:362–6).
“It’s a beautiful paper,” says Ben
Stanger, MD, PhD, from the Univer-
sity of Pennsylvania Perelman School
of Medicine in Philadelphia, who was
not involved in the study. “It reveals
that cancer cells have differential vul-
nerabilities in the epithelial versus the
mesenchymal state.”
In the study, a team from The Uni-
versity of Texas MD Anderson Cancer
Center in Houston identifi ed and
characterized highly aggressive malig-
nant cell populations that emerge dur-
ing pancreatic cancer progression.
These highly mobile and invasive
cells no longer depend on KRAS
signaling and rely on the aberrant
activation of mesenchymal programs
regulated by the chromatin remod-
eling factor SMARCB1. Mouse models
showed that Smarcb1 ablation could
intensify cancer spread; conversely,
restoring Smarcb1 slowed tumor
10 to 20. The researchers discovered
that the acoustic energy used to shear
DNA extracted from tumor tissue was
frequently turning guanine into 8-oxo-
guanine, a nucleotide that the sequenc-
ing machine read as a thymine (Nucleic
Acids Res 2013;41:e67). These G-to-T
transversions were not tumor-causing
mutations but artifacts of the sonica-
tion process.
Laurence Ettwiller, PhD, and her
colleagues from New England Biolabs
(NEB), a molecular biology reagents
company in Ipswich, MA, have now
extended those fi ndings and quanti-
fi ed the prevalence of such erroneous
variants in two widely used sequencing
datasets: the 1000 Genomes Project and
TCGA. The researchers compared the
reads of the two complementary strands
from each sequencing run to detect
aberrant transversions introduced by
DNA damage and scored the degree of
mismatching in a metric dubbed the
Global Imbalance Value (GIV).
Based upon the GIV, Ettwiller’s
team found that 41% of the datasets
in the 1000 Genomes Project con-
tained damaged samples. In TCGA,
73% of the 1,800 sequenced tumor
and healthy matched samples revealed
damage so extensive that at least half
of all the G-to-T variants were not true
mutations. Other nucleotide imbal-
ances such as C-to-T occurred at lower
but still appreciable frequencies.
According to Pugh, analytic tools
like MuTect and VarScan can correct
the problem, although not perfectly.
To eliminate the false variants, the
NEB researchers used a mix of enzymes
that repaired the DNA damage before
sequencing. “But,” says Ettwiller,
“we don’t know whether or not this
cocktail of enzymes will actually work
on the TGCA dataset,” because of dif-
ferences in experimental setup.
NEB markets the DNA-repair mix
used in the study, so the authors have
an inherent fi nancial confl ict, yet that
doesn’t bother Alexander Dobrovic,
PhD, a molecular geneticist from the
Olivia Newton-John Cancer Research
Institute in Melbourne, Australia.
“They clearly have a product to sell,
but it’s a useful product,” he says.
“We’ll be using that ourselves.”
Another workaround: molecular
barcoding, which involves adding
unique tags to each stretch of DNA so
growth and restored the cells to their
less invasive, epithelial form.
These fi ndings were supported by an
analysis of surgically resected specimens
from 134 patients with pancreatic ductal
adenocarcinoma for whom follow-up
data were available. Those whose tumors
had high levels of SMARCB1 lived, on
average, for around 14 months after
their diagnosis. In contrast, those whose
tumors had low expression levels had a
median survival of just 3.4 months.
“Those are the patients where mes-
enchymal subpopulations are promi-
nent,” says Giannicola Genovese, MD,
the study’s fi rst author. “As a result,
they do the worst.”
Gene expression profi ling revealed
that the reduction of SMARCB1
expression leads to an increase in MYC-
related activity that drives protein metab-
olism and the stress response pathways
that help the cell tolerate the increased
protein turnover.
Therein lies the cancer’s Achilles’
heel. Treatment with the drug AUY922
(luminespib; Vernalis), which blocks
HSP90, reduced cancer growth in
Smarcb1-deficient mice but not in
Smarcb1-profi cient animals. What’s
more, the therapeutic effect of AUY922
was enhanced with the addition of
drugs targeting the endoplasmic
reticulum–stress response pathway.
“We identifi ed two ways to target the
vulnerability,” says senior study author
Giulio Draetta, MD, PhD. “One is we
Pancreatic tumor cells with low Smarcb1 levels and mesenchymal markers show a greater potential to metastasize in mice (left) than cells with high Smarcb1 expression and an epithelial identity.
346 | CANCER DISCOVERY�APRIL 2017 www.aacrjournals.org
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NOTED
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The NCI launched the NCTN/NCORP Data Archive, a centralized repository of deidentified patient-level data from phase III studies carried out by groups affiliated with the National Clinical Trials Network (NCTN) and the NCI’s Community Oncology Research Program (NCORP). For information, visit https://nctn-data-archive.nci.nih.gov/.
Genome-editing tools, such as CRISPR/Cas9, have created research opportuni-ties and potential treatments for both heritable and nonheritable health condi-tions, but many people consider the genome “ethically inviolable.” However, according to a report from the National Academy of Sciences and the National Academy of Medicine, heritable germ-line editing clinical trials could one day be permitted if certain stringent criteria are met, such as the absence of reason-able alternatives and credible data on the risks and potential health benefits. The report is available at www.nap.edu.
The Cleveland Clinic opened its new Taussig Cancer Center. Costing an esti-mated $276 million, the seven-story, 377,000-square-foot facility will house all outpatient cancer treatment services, organized by cancer type. For example, all clinical and treatment areas for breast cancer will be located on the same floor to offer greater convenience for patients.