Violin plots showing changes in RNA expression (Credit: Allis lab)
Cancers emerge from many different paths. One path begins early, in embryonic development, when a protein complex called PRC2, which regulates cell differentiation, identity, and plasticity, becomes dysfunctional. PRC2 has well-established links to breast, prostate, blood, and skin cancers, among others.
Now researchers in the former Laboratory of Chromatin Biology and Epigenetics, headed by C. David Allis until his death in early 2023, have discovered surprising new details about the mechanics of this protein complex, which could potentially lead to new cancer therapies. The findings were published in Genes & Development.
It turns out that a small region of the complex long considered merely structural actually makes the entire protein function. And when researchers removed the region, called the SBD, the cancers they tested were stopped in their tracks.
"The SBD serves as a mechanical switch necessary for both healthy embryonic development and the maintenance of certain malignancies," says lead author Agata Patriotis, a former member of the Allis lab and now a postdoc at the Koch Institute for Integrative Cancer Research at MIT. "This domain could potentially be targeted by cancer inhibitors."
Off switches
Allis, a pioneer in chromatin biology, discovered that the modification of histone proteins-previously thought of as mere spools for packaging DNA in the cell nucleus of all non-prokaryotic organisms-plays a critical role in turning gene expression on and off.
One of those histone modifiers is PRC2 (polycomb repressive complex 2), an epigenetic regulator that silences certain genes during early development. It's so essential that it's found in organisms across the animal kingdom.
PRC2 manages this feat by adding a chemical marker-a methyl group-to a specific amino acid on the tail of the H3 histone (H3K27), which effectively acts as an off switch.
This protein complex is made of multiple subunits. One, called EZH2, is the part that interacts with the histone tail.
In recent years, cryo-EM structural studies showed that a specific region of the EZH2 subunit, called the SBD, bends and changes shape when the protein is activated. It was unexpected-a shape shift suggested that the SBD wasn't an inert bit of EZH2's architecture, as had long been assumed, but instead functional in some way.
It was Allis who suggested that Patriotis investigate what SBD's might be doing.
"Dave was very curious about histone modifications, and he was particularly excited about this research's potential to discover something fundamental about PRC2," Patriotis says.
Functional necessity
For the current study, the researchers deleted SBD from the protein complex to see what the impact might be. Despite its absence, PRC2 remained intact, demonstrating that SBD wasn't essential to its architectural integrity.
That was surprise number one. "Our hypothesis had been that the SBD was important for stability and that the complex wouldn't be able to assemble without it, but that turned out to not be true," Patriotis says.
Surprise number two came when they discovered that the SBD was, however, critically important to PRC2's ability to function-without it, it could not do its main job of repressing the activation of certain genes. Specifically, the absence of the SBD prevented the complex from methylating its target histone, H3K27, and therefore certain genes were missing their off switches.
"The SBD domain has a really fundamental role in regulating the whole complex," says Patriotis. "Its absence prevents the EZH2 enzyme from spreading repressive chemical marks across the genome."
A new inhibition target
Because mutations in the EZH2 subunit are linked to a number of cancers, they next investigated the impact a missing SBD might have on the proliferation of cancer cells. Remarkably, they found that removing the SBD halts the growth of aggressive lymphomas driven by EZH2 mutations. It also normalizes gene expression, mimicking the effects of powerful clinical cancer inhibitors.
"The SBD domain could potentially be used to inhibit the enzymatic activity of PRC2," Patriotis says. "It's a vulnerable interface."
For Patriotis, this study continues the Allis lab's legacy of producing fundamental biological insights. "David very much cared about gene expression and transcription in terms of histone function," she notes. "But he also believed there was something special about every single enzyme that is shared across the biosphere. Those molecules, like PRC2, really tell you what has fundamental importance and what doesn't."
