Illuminating Aberrant mRNA Events in CLL

Although much attention has been paid to genetic changes, chiefly DNA mutations, as potential drivers of tumorigenesis, RNA is coming into the spotlight as another key player to consider. According to a recent study from Memorial Sloan Kettering Cancer Center in New York, NY, intronic polyadenylation (IPA)—a form of mRNA processing that generates truncated transcripts—is widespread in chronic lymphocytic leukemia (CLL) and can target tumor suppressor genes. The findings suggest that this disease, associated with few mutations, may be promoted by nongenetic events.

“A few years back, we developed a method to identify the 3′ end of every mRNA in the transcriptome,” says senior author Christine Mayr, MD, PhD. “We noticed that many 3′ ends occurred within introns and, using computational tools and RNA sequencing, validated more than 4,000 of these IPA isoforms. We think IPA may contribute to a more diverse proteome, at least in normal cells.”

Wondering whether IPA might be exploited by cancer, Mayr and her group compared normal and malignant B cells from 59 patients with CLL. They pinpointed 330 significantly upregulated IPA isoforms in the malignant cells, resulting in shorter proteins with altered functions. For instance, truncated DICER and FOXN3 were no longer effective tumor suppressors. Aberrant IPA also yielded oncogenic effects: The shorter form of CARD11, which is more stable than its full-length counterpart, more potently turned on NFκB signaling, helping lymphocytes survive and proliferate. Additionally, truncated MGA overrode the normal protein's role of keeping MYC signaling in check.

“Importantly, we saw that in different patients, the same gene could be targeted either by mutations or [its transcript] by IPA,” Mayr says. Considerably more patients (up to 85%) had tumor suppressor genes affected at the level of mRNA rather than DNA (up to 2%)—a population hitherto likely missed by genome-wide sequencing efforts in precision medicine, she notes.

Focusing on the most prevalent IPA isoforms in their study—a total of 199, derived from 190 genes—the team examined a database of genomically sequenced solid tumors and found that 72% of these genes were known targets of inactivating mutations. “This gives us a list of novel tumor suppressor candidates in CLL whose functional loss is, instead, nongenetically driven,” Mayr observes. She had suspected that, by affecting a given tumor suppressor gene, IPA could be cancer-relevant, “but I never expected it to be so extensive,” she adds.

“The sheer number of IPA targets in CLL is remarkable; it wasn't obvious a priori that there would be so many,” agrees Charlotte Kuperwasser, PhD, of Tufts University School of Medicine in Boston, MA. In 2016, she and her group published one of the first studies showing that IPA generates a truncated, oncogenic form of MAGI3 that helps drive neoplastic transformation in breast cancer. “It was exciting to see MAGI3 also identified in CLL, as this validates our results on a large scale,” she adds.

Overall, “this study fits well with previous work showing how RNA processing abnormalities, at both the levels of splicing and mRNA 3′-end formation, can contribute to cancer development,” says Michael Green, MD, PhD, of the University of Massachusetts Medical School in Worcester. “From a mechanistic point of view, it will be very interesting to determine the molecular basis for IPA being widespread in CLL.”

It's also worth probing whether any of the genes controlling IPA are themselves targets of, for instance, copy-number changes or chromosomal rearrangements, Kuperwasser observes. “If so, these could represent ‘hidden drivers’ that, by participating in aberrant IPA, contribute to the panoply of altered proteins in cancer pathogenesis. Such genes would be attractive therapeutic targets.”

Mayr hopes her work inspires follow-up research from others in the field. “The more of these studies there are,” she says, “the more likely it is that we'll realize the need to go beyond genomic analyses in cancer diagnostics.” –Alissa Poh