Cancer results from a combination of uncontrolled proliferation and survival as well as a block in differentiation which keeps the cancer cells in an immature state. All of these attributes are normal cellular processes that have been hijacked by the cancer cell for its own purposes. In order to understand cancer and to develop effective targeted therapies, it is necessary to have a greater understanding of these hijacked cellular processes.
Much of our understanding of cancer comes from studying changes in the DNA genetic code of cancer cells. However, rather than merely changing the genetic code, other events may also contribute to cancer. Recent studies of acute myeloid leukemia (AML) patients have highlighted that AML may stem from alterations in how genes are expressed from DNA. Interestingly, these studies show that AML patients are unique amongst other cancers in that they frequently harbor mutations in the “epigenome” and “RNA splicing,” which are part of the cellular machinery that regulates which proteins are ultimately expressed in the cell.
The epigenome refers to the combination of DNA along with the proteins bound to DNA and reversible chemical changes to DNA known as DNA methylation. The proteins and chemical changes surrounding DNA control which genes are turned on and off in a cell. Once a gene is expressed from DNA, the ensuing message, known as RNA, must undergo removal of segments of its sequence to be converted into the final product, known as protein. The machinery which carries out this process of removing segments of RNA is known as RNA splicing. Our understanding of how mutations in the epigenetic and RNA splicing machinery contribute to AML remains a mystery.
New Research Demonstrating Cooperation of Oncogenic Drivers
A team led by Omar Abdel-Wahab at Memorial Sloan Kettering Cancer Center (MSK) has now identified how alterations in the epigenetic and RNA splicing processes work together to drive AML development. This research was published in the October 2, 2019 issue of Nature and was a combined effort between the group at MSK, led by Akihide Yoshimi, Adrian Krainer’s lab at Cold Spring Harbor Laboratory led by Kuan-Ting Lin, and Daniel Wiseman of the University of Manchester.
Using publicly available databases of RNA sequencing of AML patients, including the Beat-AML dataset (funded by The Leukemia & Lymphoma Society), the team showed that an RNA splicing factor known as SRSF2 is recurrently mutated in AML. However, they made the unexpected discoveries that these SRSF2 mutations are more common than previously anticipated in AML and that mutations in SRSF2 commonly overlap with mutations in a protein called IDH2. In fact, there is a 50% chance that when SRSF2 is mutated, IDH2 is also mutated (and vice versa).
In order to understand why these mutations frequently overlap in AML patients, the team expressed both mutations in normal blood stem cells. Mutations in either SRSF2 or IDH2 lead to alterations in normal blood stem cell function but do not lead to leukemia. However, simultaneous mutation of both genes generates leukemia.
Changes in RNA splicing modifies the RNA composition in the cell. Dr. Abdel-Wahab’s team demonstrates that a likely contributor to leukemogenesis caused by mutations in both SRSF2 and IDH2 is a reduction in a transcriptional regulator called INTS3. The cause of INTS3 reduction is through an aberrant splicing event that leads to premature degradation of the INTS3 RNA. The team further identifies that the mechanism of INTS3 reduction is through the coordinate action of mutant SRSF2 and IDH2.
A reduction in INTS3 likely results in alterations in transcriptional activity in the cell. Indeed, transcriptional profiling in SRSF2/IDH2 double mutant cells show that INTS3 loss has an effect on blood cell differentiation programs. This correlates the reduction of INTS3 with cellular alterations directly associated with leukemogenesis. The team therefore demonstrates that IDH2-induced changes to the epigenome alter SRSF2-induced RNA splicing in a way that drives the development of leukemia.
Beyond Blood Cancer
Having identified a critical role of INTS3 in IDH2/SRSF2 double-mutant cells, Dr. Abdel-Wahab’s team asked whether mutant IDH2 may affect splicing in other cancers. The team looked at splicing in a type of brain cancer called glioma, where many patients have mutations in IDH2 and the related protein IDH1. In IDH2 and IDH1 mutant low-grade gliomas, there are aberrant splicing events, and a significant number of these events are also seen in IDH2 mutant AML. It remains to be seen whether there are any enhanced splicing events when mutant IDH2 is in combination with mutant SRSF2 or any other RNA splicing regulators. These observations indicate that mutant IDH proteins may show similar effects in two diverse cell types and suggest that this phenomenon may be found in other tumors as well.
How this Research may Help AML Patients
These findings open up many questions about how changes to the epigenome might alter gene expression through changing RNA splicing. In addition, these findings have potential implications for treatment as there is already an FDA approved inhibitor of mutant IDH2 for AML patients. Given the frequent co-occurrence of mutations in SRSF2 with mutations in IDH2, it will also be very important to determine if altered RNA splicing can be targeted as a new therapeutic for AML patients. This is a key ongoing effort by this team. In fact, the co-authors in this study from Cold Spring Harbor Laboratory have pioneered the first FDA-approved drug targeting mis-splicing in human disease. It will now be exciting to see if similar approaches can be used to treat patients with blood cancers harboring mutations in RNA splicing.
Dr. Akihide Yoshimi is supported by The Leukemia & Lymphoma Society through a Career Development Program Special Fellow Award.
Dr. Omar Abdel-Wahab is supported by The Leukemia & Lymphoma Society through a Career Development Program Scholar in Clinical Research Award.
Yoshimi A, Lin K-T, Wiseman, DH et al. Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis. Nature. Published online October 2, 2019.