John Essigmann - New evidence for how a rare form of liver cancer arises
MIT team finds mechanism by which exposure to vinyl chloride may produce cancerous mutations.
Anne Trafton | MIT News Office
April 1, 2015
the 1970s, epidemiologists found that workers in factories using vinyl
chloride, the key ingredient for PVC plastics, had unusually high rates
of a rare form of liver cancer called angiosarcoma.
Biologists later identified a mutation that appears to be associated
with this cancer, which originates in cells of the blood vessels that
feed the liver. Now, using new sequencing technology that enables
large-scale analysis of DNA damage-associated mutations, MIT researchers
have pinpointed the specific type of DNA damage that may be responsible
for this mutation.
With this knowledge, scientists could develop tests to monitor
workers who might be exposed to vinyl chloride, because it has been
previously shown that this type of DNA damage can be detected as a
biomarker in urine samples. This could alert factories that they need to
improve their safety practices if their workers are being exposed to
too much vinyl chloride.
The research also lays the groundwork for applying this technology to
identify other types of DNA damage, also called DNA lesions or adducts,
that may be responsible for certain types of cancers. The initiation of
many cancers may arise from the mutations generated by DNA lesions that
are produced by natural processes such as inflammation, or by exposure
to environmental agents such as vinyl chloride. These processes generate
a variety of DNA lesions, making the identification of the most
significant lesion a challenging task.
“I can think of a dozen different lesions this technology could be
applied to,” says John Essigmann, the William R. and Betsy P. Leitch
Professor of chemistry and a professor of toxicology and biological
engineering. “Unfortunately there are a lot of things in the environment
that are potentially associated with disease, and many of them do so by
damaging nucleic acids.”
Essigmann, director of MIT’s Center for Environmental Health
Sciences, is the senior author of this study, which was published in the
April 1 issue of the journal Nucleic Acids Research. The paper’s lead author is Shiou-chi (Steven) Chang, a graduate student in biological engineering.
Vinyl chloride is believed to cause many different types of DNA
damage, but until now scientists had been unsure which of those lesions
were most likely to produce cancers such as hepatic angiosarcoma. These
lesions are formed when metabolic byproducts of vinyl chloride react
chemically with the bases that encode the genetic information in DNA.
Scientists studying this type of cancer narrowed the suspects down to
a group of lesions called etheno adducts, which contain an extraneous
carbon-carbon double bond added to the regular DNA bases. There are four
different versions of etheno adducts: One that forms on the DNA base
adenine, one that involves cytosine, and two different versions that
About 10 years ago, Essigmann’s lab published a paper analyzing the
mutagenic potential of ethenoadenine and ethenocytosine. For that study,
they had to introduce the lesions into cells one by one and analyze
each sample individually, which is a very time-consuming process.
In the past few years, the MIT team, led by Chang, adopted and
improved a previously described next-generation sequencing approach,
which allows for simultaneous analysis of many DNA strands. With the new
system, “just by doing one sequencing reaction, you can get all of the
data that might have taken weeks or months in the past,” Chang says.
Using this system, the researchers have completed the study of all
four etheno adducts, using E. coli that vary in their DNA repair and
“With this method, you can study several DNA lesions all at the same
time. You’re able to make a side-by-side comparison, which is always
better than measuring one thing, and measuring another thing a few
months later, and then another one after that,” Essigmann says. “We can
do them all at once but get exactly the same high-quality information.”
The researchers found that one of the ethenoguanine lesions, known as N2,3-ethenoguanine,
cannot be repaired by an enzyme known as AlkB, unlike the other three
etheno adducts. This could explain why this particular DNA damage is the
most prevalent etheno lesion and remains in cells for a long time. When
the damaged DNA is copied, enzymes responsible for copying DNA may
insert the wrong nucleotide opposite the lesion, which causes a guanine
to adenine mutation.
Previous work has shown that this type of mutation, when it occurs in
a specific stretch of a cancer-promoting gene known as K-ras, is
associated with hepatic angiosarcoma.
“This is exciting new data that has redefined the role of etheno DNA
adducts in mutagenesis and carcinogenesis,” says Ian Blair, director of
the Center for Cancer Pharmacology at the University of Pennsylvania
School of Medicine, who was not part of the research team. The findings
should stimulate new interest in analyzing urinary concentrations of
etheno DNA adducts in human populations, he adds.
From bacteria to humans
Although these studies were done in E. coli cells, all of the enzymes
studied, such as AlkB and the enzymes that introduce errors while
copying damaged DNA, have human homologs. “Understanding how it works in
E. coli, although it’s not human cells, may be a good model for
understanding what may happen in humans,” Chang says.
The researchers are now analyzing other types of DNA lesions,
including those caused by butadiene, a carcinogenic chemical found in
tobacco and gasoline. They are also working on ways to adapt the system
to study mammalian cells. Using the CRISPR/Cas9 gene-editing system, the
team hopes to test what happens to particular DNA lesions in mammalian
cells that differ in their DNA repair enzymes and DNA-copying enzymes.
The study was funded by the National Institutes of Health. Other MIT
authors of the paper are research associate Bogdan Fedeles; research
scientist Jie Wu; research affiliates Vipender Singh, James Delaney, and
Deyu Li; undergraduate Emily Yau; graduate student Marco Jost;
chemistry professor Catherine Drennan; and Stuart Levine, associate
director of MIT’s BioMicro Center. F. Peter Guengerich, Linlin Zhao,
Plamen Christov, Lawrence Marnett, and Carmelo Rizzo of Vanderbilt
University are also authors of the paper.