Leonid Mirny - Seeing cancer in three dimensions
Scientists find that the 3-D structure of a cancer cell’s chromosomes plays a big
role in which genes get deleted or copied.
Anne Trafton, MIT News Office
November 21, 2011
One of the hallmarks of cancer cells is that certain
regions of their DNA tend to get duplicated many
times, while others are deleted. Often those genetic
alterations help the cells become more malignant —
making them better able to grow and spread
throughout the body.
Now, a team of MIT and Harvard University
researchers has found that the three-dimensional
structure of the cell’s genetic material, or genome,
plays a large role in determining which sections of
DNA are most likely to be altered in cancerous cells.
The researchers, led by Leonid Mirny, an associate
professor of physics and health sciences and
technology, developed a technique to compare the
3-D architecture of chromatin to the chromosomal
aberrations often seen in cancer. In the new study,
they showed that any two points that routinely
encounter each other are more likely to form the end
of a DNA loop that gets cut out or duplicated.
“It looks very much like the chromosomal
aberrations in cancer, to a large extent, are shaped
by the chromosome’s structure,” Mirny says.
The findings, described in the Nov. 20 issue of
Nature Biotechnology, reveal mechanisms and
underlying physical principles governing genome alterations in cancerous cells, and could help pinpoint locations
that host undiscovered cancer-causing or tumor-suppressing genes.
A new dimension
In 2009, a team of scientists — including Mirny and colleagues from MIT, the Broad Institute, the University of
Massachusetts Medical School (UMMS), and Harvard — reported the first three-dimensional view of the human
genome. Using an experimental technique called Hi-C, developed in the labs of the Broad Institute’s Eric Lander
and Andreas Gnirke and UMMS’ Job Dekker, and simulations developed in the Mirny lab, they found that the
genome is organized in a structure known as a “fractal globule.” This arrangement enables the cell to pack DNA
incredibly tightly while avoiding the knots and tangles that might interfere with the cell's ability to read its own
Mirny and his colleagues had no plans to use Hi-C to study alterations of the genome in cancer until a
serendipitous conversation arose with scientists at the Broad Institute. Those researchers, including Gad Getz,
the director of Cancer Genome Computational Analysis at the Broad, and Matthew Meyerson, a senior associate
member of the Broad and professor of pathology at Harvard Medical School, were studying genetic mishaps —common in cancer cells — known as single copy number alterations (SCNAs).
SCNAs can be deletions of a large region of DNA or duplications of a region — meaning they could play some role
in cancer, since it’s advantageous for a cancer cell to have many copies of stretches containing oncogenes
(cancer-causing genes), or to delete stretches with tumor-suppressing genes.
Getz and colleagues at the Broad had shown that the probability that a particular stretch of DNA will be duplicated
or excised is inversely proportional to its length. When Mirny looked at their findings, he noticed a striking
similarity to the Hi-C data: The probability that two particular spots on a chromosome will come into proximity with
each other is also inversely proportional to the length of the DNA between them.
Mirny and Getz decided to test the hypothesis that the three-dimensional structure of the chromosome influences
the likelihood of a particular stretch of DNA being copied or deleted. To do that, they compared the structure of
chromatin predicted by the fractal-globule model with the locations of common SCNAs found in 3,000 cells
exhibiting 26 different types of cancer.
What they found confirmed this idea. “What we see by mathematical modeling is that the probability of two points
coming together in the 3-D structure is very close to the probability of a loop of that length to be amplified or
deleted,” Mirny says
“It gives even more evidence to the notion that the physical colocation of otherwise disparate regions of the
genome in the cell is the source of errors that arise,” says Levi Garraway, an assistant professor of medicine at
Harvard Medical School and a member of the Broad Institute and Dana-Farber Cancer Institute who was not
involved in this research.
DNA repair gone wrong
This work also suggests a possible mechanism by which SCNAs may occur: When two points are in contact with
each other, there is a greater chance that these points may be joined by mistake during DNA repair.
When DNA suffers a break, special enzymes move in to repair it. If two points near each other are being repaired
at the same time, the enzymes may accidentally attach them to each other, creating a loop that gets cut out of the
genome, says Geoff Fudenberg, a graduate student at Harvard and lead author of the paper.
This explains how excisions might occur, but the researchers believe that the mechanism of creating duplications
is likely more complicated.
In this study, the researchers also investigated the likelihood of these alterations spreading through a population
of cancer cells. It was already known that alterations beneficial to the cancer cell are more likely to spread
through the population, while those that are detrimental get eliminated. There is also a third class of mildly
damaging mutations called “passenger mutations.” In this study, the researchers found evidence that these
mutations also can be selected against. Specifically, the longer the alteration, the more likely it was to be
In future studies, the team plans to analyze 3-D genome models of different cancer types, to see if the alterations
likely to occur in liver cancer, for example, differ from those that would occur in lung cancer.
“The more you know about mutational mechanisms, and the more you understand the landscape of possible
mutations in cancer, the better job you’re going to do at finding genes that are really helping the cancer, and the
better you’ll be able to target those,” Fudenberg says.
Mirny and Fudenberg are members of MIT's Center for Physical Sciences in Oncology, funded by the National