MIT Research News' Journal

New analysis reveals tumor weaknesses

Scientists have known for decades that cancer can be caused by genetic mutations, but more recently they have discovered that chemical modifications of a gene can also contribute to cancer. These alterations, known as epigenetic modifications, control whether a gene is turned on or off.

Analyzing these modifications can provide important clues to the type of tumor a patient has, and how it will respond to different drugs. For example, patients with glioblastoma, a type of brain tumor, respond well to a certain class of drugs known as alkylating agents if the DNA-repair gene MGMT is silenced by epigenetic modification.

A team of MIT chemical engineers has now developed a fast, reliable method to detect this type of modification, known as methylation, which could offer a new way to choose the best treatment for individual patients.

“It’s pretty difficult to analyze these modifications, which is a need that we’re working on addressing. We’re trying to make this analysis easier and cheaper, particularly in patient samples,” says Hadley Sikes, the Joseph R. Mares Assistant Professor of Chemical Engineering and the senior author of a paper describing the technique in the journal Analyst.

The paper’s lead author is Brandon Heimer, an MIT graduate student in chemical engineering.

Beyond the genome

After sequencing the human genome, scientists turned to the epigenome — the chemical modifications, including methylation, that alter a gene’s function without changing its DNA sequence.

In some cancers, the MGMT gene is turned off when methyl groups attach to specific locations in the DNA sequence — namely, cytosine bases that are adjacent to guanine bases. When this happens, proteins bind the methylated bases and effectively silence the gene by blocking it from being copied into RNA.

“This very small chemical modification triggers a sequence of events where that gene is no longer expressed,” Sikes says.

Current methods for detecting cytosine methylation work well for large-scale research studies, but are hard to adapt to patient samples, Sikes says. Most techniques require a chemical step called bisulfite conversion: The DNA sample is exposed to bisulfite, which converts unmethylated cytosine to a different base. Sequencing the DNA reveals whether any methylated cytosine was present.

However, this method doesn’t work well with patient samples because you need to know precisely how much methylated DNA is in a sample to calculate how long to expose it to bisulfite, Sikes says.

“When you have limited amounts of samples that are less well defined, it’s a lot harder to run the reaction for the right amount of time. You want to get all of the unmethylated cytosine groups converted, but you can’t run it too long, because then your DNA gets degraded,” she says.

Rapid detection

Sikes’ new approach avoids bisulfite conversion completely. Instead, it relies on a protein called a methyl binding domain (MBD) protein, which is part of cells’ natural machinery for controlling DNA transcription. This protein recognizes methylated DNA and binds to it, helping a cell to determine if the DNA should be transcribed.

The other key component of Sikes’ system is a biochip — a glass slide coated with hundreds of DNA probes that are complementary to sequences from the gene being studied. When a DNA sample is exposed to this chip, any strands that match the target sequences are trapped on the biochip. The researchers then treat the slide with the MBD protein probe. If the probe binds to a trapped DNA molecule, it means that sequence is methylated.

The binding between the DNA and the MBD protein can be detected either by linking the protein to a fluorescent dye or designing it to carry a photosensitive molecule that forms hydrogels when exposed to light.

This technique, which cuts the amount of time required to analyze epigenetic modifications, could be a valuable research tool as well as a diagnostic device for cancer patients, says Andrea Armani, a professor of chemical engineering and materials science at the University of Southern California, who was not part of the research team.

“It’s a really innovative approach,” Armani says. “Not only could it impact diagnostics, but on a broader scale, it could impact our understanding of which epigenetic markers are linked to which diseases.”

The MIT team is now adapting the device to detect methylation of other cancer-linked genes by changing the DNA sequences of the biochip probes. They also hope to create better versions of the MBD protein and to engineer the device to require less DNA. With the current version, doctors would need to do a surgical biopsy to get enough tissue, but the researchers would like to modify it so the test could be done with just a needle biopsy.

The research was funded by a David H. Koch fellowship, a National Science Foundation fellowship, a Burroughs Wellcome Fund Career Award, the National Institute for Environmental Health Sciences, and the James H. Ferry Fund for Innovation.

Finding a piece of the proton-spin puzzle

What causes a proton to spin?

This fundamental question has been a longstanding mystery in particle physics, although it was once thought that the answer would be fairly straightforward: The spin of a proton’s three subatomic particles, called quarks, would simply add up to produce its total spin.

But a series of experiments in the 1980s threw this theory for a loop, proving that the spins of the quarks are only partially responsible for the proton’s overall spin. Thus emerged what physicists now refer to as the “proton spin crisis,” prompting a decades-long search for the missing pieces, or contributors, to a proton’s spin.

Now an international team of more than 300 researchers, including MIT physicists, has placed new constraints on the spin of the proton’s antiquarks — the antiparticles of quarks that are thought to arise when the bonds between quarks break. The researchers say these measurements may help to identify the antiquark’s role in the proton’s spin, as well as the mechanism by which antiquarks are produced.

“We’d like to understand the spin contributions of the subatomic particles inside the proton, to learn something fundamental about their interactions,” says Justin Stevens, a postdoc in MIT’s Laboratory for Nuclear Science (LNS). “Now we have a new method sensitive to the antiquark spin, which can shed light on where these quarks and antiquarks come from.”

Stevens and Jan Balewski, a research scientist in the LNS, led the analysis of more than 1 billion recorded proton collisions produced by the Relativistic Heavy Ion Collider (RHIC), a particle accelerator at Brookhaven National Laboratory. Using the facility’s STAR detector, which tracks the particles produced by each collision, the team identified 3,500 proton collisions that produced a W boson — an elementary particle that, when generated, temporarily inherits the spin of a proton’s antiquark.

“We measured the decay product of the W boson, and from this, we could infer the spin of the antiquark, and how it relates to the spin of the mother proton,” Balewski explains. “It turns out the antiquark polarization is marginal, and contributes very little to the polarization of the proton.”

Stevens, Balewski, and their collaborators publish their experimental results today in the journal Physical Review Letters.

When protons collide

According to the Standard Model of particle physics, the proton is a composite particle composed of three quarks, each of a distinct type, or “flavor”: two “up” quarks, and one “down” quark. These quarks are bound together by particles called gluons which, when temporarily broken, are thought to give rise to pairs of short-lived quarks and antiquarks. Since a proton’s spin cannot be fully explained by the spin of its quarks, physicists have looked to other possible contributors, such as the spins of gluons and antiquarks, or their orbital motion inside the proton.

Stevens, Balewski, and their colleagues identified the antiquarks by measuring the decay of W bosons following collisions of polarized protons. As Balewski explains it, at any given moment, a polarized or spinning proton contains pairs of quarks and antiquarks that “pop out and disappear, pop out and disappear.”

“When they show up, the spin of the proton is passed to those antiquarks to some degree,” Balewski says. “Now this antiquark, for a fraction of a second, shows up in the proton exactly at the moment when this proton collides with this other proton, and the W boson is produced.”

The researchers observed a significant difference in the number of W bosons produced when the proton’s spin was oriented in the same direction as its motion compared to cases where the proton’s spin was oriented in the opposite direction. The antiquark spin was then inferred by measuring this difference for various orientations of the electrons produced as the W boson decays.

Exploring antiquarks’ origins

The researchers’ results provide significant new constraints on the spin of the proton’s antiquarks, which contribute a small fraction to the total spin of the proton. In addition, they observed a slightly larger-than-expected spin effect for a subset of up-flavored antiquarks compared to down-flavored antiquarks. Stevens says this asymmetry in antiquark spin may help to identify how a proton’s antiquarks arise in the first place.

“The naive picture of how these quark/antiquark pairs pop in and out of existence is that gluons split to form these pairs,” Stevens says. “But if that were the case, you’d expect to get equal numbers of up- and down-flavored quarks. Our measurements provide some new information, which could tell us something about how these quarks and antiquarks are produced.”

Marco Stratmann, a staff scientist at the Institute for Theoretical Physics at the University of Tubingen, says the group’s data “provide us with ‘snapshots’ of the proton’s spin and flavor structure. … In [future] analyses of the proton’s spin structure, this data will provide a novel and particularly clean probe of the up and down antiquark polarizations, largely free of theoretical uncertainties.”

“We’re tightening up the constraints on what this antiquark polarization looks like,” Stevens says. “And with future data, that constraint will get even better.”

This research was supported in part by the National Science Foundation and the U.S. Department of Energy.