Study sheds new light on molecular pathways behind marrow disorders

How a single alteration in fundamental cellular machinery drives blood diseases and cancers
Illustration of RNA splicing
A study published Monday by Fred Hutch's Dr. Robert Bradley and colleagues offers the first glimpse of the molecular pathways that link RNA splicing to myelodysplastic syndrome, a disorder akin to leukemia. Illustration by Kimberly Carney / Fred Hutch News Service

Our bone marrow is a veritable workhorse — the spongy tissue packed inside bones churns out 1 trillion blood cells every day. Sometimes, one of those many cell divisions goes wrong in a certain way, resulting in leukemia, lymphoma or other bone marrow diseases.

Researchers have now uncovered how a single mutation can trigger myelodysplastic syndrome, or MDS, a disorder akin to leukemia in which the bone marrow overproduces some blood cell precursors but can’t convert them to healthy blood cells. This mutation is surprising because it causes an alteration in one of life’s most fundamental processes, said Dr. Robert Bradley, a molecular biologist at Fred Hutchinson Cancer Research Center who led the study along with Dr. Omar Abdel-Wahab of Memorial Sloan Kettering Cancer Center and Dr. Stephanie Halene of Yale University.

In a paper published Monday in the journal Cancer Cell, Bradley and his colleagues describe the link between MDS and that mutation, which occurs in a single gene involved in processing RNA, the go-between molecule that conveys genetic information from DNA to protein production.

The study is the first glimpse of the molecular pathways that link RNA splicing to MDS, and that’s important because understanding the biology that drives this disease is essential to improving treatments, Bradley said. Right now, bone marrow transplantation is the only cure for MDS, but most patients are not eligible for transplants due to age or poor health. Only 35 percent of U.S. patients will survive three years beyond diagnosis, according to a 2007 study, and about a third of MDS patients go on to develop acute myeloid leukemia.

“There are very few drugs to treat these diseases, and the available ones don’t work well,” Bradley said. “A large part of the reason is because we didn’t know how the disease is happening.”

The mutated gene is called SRSF2, and it codes for a piece of the machinery that splices RNA, a process in which RNA is cut and stitched back together, editing out pieces that aren’t needed to make the final protein. About 90 percent of human genes are spliced, Bradley said, and it’s not intuitive that altering RNA splicing would lead to cancer or MDS.

“A lot of people, myself included, would have expected it would just kill the cells if you mutated these proteins. But that doesn’t appear to be the case,” he said.

About 60 percent of patients with MDS have mutations in genes involved in RNA splicing, and up to 50 percent of patients with the MDS-like disease chronic myelomonocytic leukemia carry SRSF2 mutations. Splicing component mutations are also common in other leukemias, such as chronic lymphocytic leukemia, and in the eye cancer known as uveal melanoma, and occur less frequently in lung and breast cancers.

Dr. Robert Bradley
Fred Hutch's Dr. Robert Bradley led the study in collaboration with researchers at Memorial Sloan Kettering Cancer Center and Yale University. Photo by Robert Hood / Fred Hutch News Service

A first step toward targeted therapy

The MDS-linked mutation in SRSF2 was discovered in 2011 as part of a large research effort to sequence the genomes from cancerous cells (and those of related diseases, like MDS). For the most part, those newly revealed sequences primarily uncovered mutations already known to be linked to cancer, Bradley said, but they did find a few surprises — like the ties between RNA splicing and cancer.

“The reason it was so mysterious is that a lot of known cancer-causing mutations sort of make sense,” he said, meaning such mutations cause cellular changes inherent to cancer, like releasing the brakes on cell division or eliminating checkpoints on faulty chromosomes.

“It was very surprising and not obvious how a mutation in a protein that catalyzed RNA splicing would cause cancer or myelodysplasias, partly because splicing is such a fundamental process,” Bradley said.

To unpick the links from RNA splicing to disease, the researchers replicated the most common SRSF2 mutation in certain bone marrow cells in mice. They found that simply introducing that mutation spurred overgrowth of blood cell precursors, just like in MDS, showing that this mutation is truly driving the disease and not simply along for the ride.

They also found that mice missing SRSF2 entirely also have problems producing blood cells, but their disease looked different from those with the MDS-linked mutation, meaning that mutation does something other than disabling the splicing protein. Looking more closely at the RNA affected by this mutation, they saw that about 700 genes are differently spliced in the presence of mutant SRSF2 — meaning, presumably, the proteins produced by those hundreds of genes are also altered in diseased cells.

It sounds dramatic, but 700 genes is a relatively subtle effect, Bradley said, given that SRSF2 is required for thousands of splicing events. When they removed the protein entirely from cells, thousands and thousands of genes were affected.

“In a sense that’s the mystery,” Bradley said. “Splicing does affect [nearly] all genes, but you can introduce these splicing factor mutations and the cell is fine. In fact it’s able to outcompete other cells.”

Looking more carefully at those genes in the mutant mice and in people with MDS or leukemia, the researchers found that a gene known to be involved in MDS and many cancers, EZH2, is also affected by the mutated SRSF2. EZH2’s altered splicing in these mutant cells results in lower levels of the EZH2 protein, and the researchers found they could partly reverse the malignancy-driving effects of mutant SRSF2 by adding extra EZH2 to cells.

Understanding, one by one, the molecular changes that connect the SRSF2 mutation to disease “is the required first step to develop a targeted therapy,” Bradley said.

And that’s his team’s next goal. Bradley is optimistic about the prospect of eventually finding a therapy that could block one of these steps — molecules already exist that prevent splicing factors from binding to RNA, and he and his colleagues are now asking whether they can alter those molecules so they affect only the disease-driving SRSF2, leaving healthy splicing to proceed and, hopefully, reverse the disease.

Rachel Tompa is a former staff writer at Fred Hutchinson Cancer Center. She has a Ph.D. in molecular biology from the University of California, San Francisco and a certificate in science writing from the University of California, Santa Cruz. Follow her on Twitter @Rachel_Tompa.

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