Potential Driver Mutations Identified in CLL

Catherine J. Wu, MD

Dozens of genetic abnormalities, including 44 mutated genes and 11 recurrent somatic copy number variations, were found to potentially play a role in progression and/or relapse of chronic lymphocytic leukemia (CLL), according to a recent study published in Nature.

Two of the mutations, RPS15 and IKZF3, were not previously associated with human cancer. It was also found that patients with mutations TP53 or SF3B1 tended to produce shorter remissions after therapy.

“Sequencing the DNA of CLL has taught us a great deal about the genetic basis of the disease,” said senior study author Catherine J. Wu, MD, an associate professor of Medicine at Dana-Farber Cancer Institute, the Broad Institute of MIT and Harvard, and Brigham and Women’s Hospital, in a statement. “Previous studies, however, were limited by the relatively small number of tumor tissue samples analyzed, and by the fact that those samples were taken at different stages of the treatment process, from patients treated with different drug agents."

The Nature study analyzed genetic material in CLL and tissue from more than 538 patients, 278 of whom were enrolled in the phase III CLL8 study, which established the combination of fludarabine, cyclophosphamide, and rituximab (Rituxan) as the current standard-of-care first-line regimen, to help determine standard treatment for the disease. Whole-exome sequencing was performed on each sample.

“In our new study, we wanted to determine if analyzing tissue samples from a large, similarly-treated group of patients provides the statistical power necessary to study the disease in all its genetic diversity–to draw connections between certain mutations and the aggressiveness of the disease, and to chart the emergence of new mutations and their role in helping the disease advance,” Wu said. “Our results demonstrate the range of insights to be gained by this approach.”

Tumor samples included previously unrecognized putative cancer drivers (RPS15, IKZF3), and collectively identify RNA processing and export, MYC activity, and MAPK signaling as central pathways involved in CLL.

In the drivers not previously associated with cancer, RPS15 was found to be recurrently mutated (n = 23, 4.3%), while substitutions of recurrent LI62R were also found (n = 11, 2.0%) in IKZF3, suggesting that this gene is a key transcription factor in B-cell development, and its upregulation has been associated with adverse outcome, the authors noted.

Driver genes discovered to modulate MYC activity included MGA (n = 17, 3.2%), PTNP11 (n = 7, 1.3%) and FUBP1 (n = 9, 1.7%).

Data also showed that 8.7% of patients harbored mutations in the MAPK-ERK pathway, including RAS (NRAS, n = 9, and KRAS, n = 14, totaling 4.1%), BRAF (n = 21, 3.7%), or MAP2K1 (n = 12, 2%). A subset of these patients had new types of molecular errors that allow the MYC cancer gene to become overactive.

In terms of clinical outcome, shorter progression-free survival was associated with TP53 and SF3B1 mutations, and of the newly identified recurrent lesions evaluated, a shorter PFS was observed in patients with RPS15 (P = .024).

Through targeted deep sequencing, researchers screened for relapse drivers in 11 of the 41 pretreatment samples in which whole-exome sequencing did not detect the relapse driver. In 7 of these 11 CLLs, at least one relapse driver was detected in the pretreatment sample.

In a comparison of pretreatment and relapse cancer-cell fraction (CCF) for each driver, the researchers observed three general patterns. Tri(12), del(13q) and del(11q), suggested as early drivers, tended to remain stably clonal despite marked, often branched, evolution, confirming that these are early events likely shared by the entire malignant population, the authors noted.

TP53 mutations and del(17p) demonstrated increases in CCF upon relapse, suggesting a fitness advantage under therapeutic selection. The novel driver IKZF3 increased in CCF in three of four relapse cases, remaining clonal in the fourth, supporting the suggestion that these mutations probably enhance fitness.

Moreover, mutations in SF3B1 and ATM seemed as likely to decline in CCF as they were to increase, the authors noted. These results suggest that such mutations do not provide the same strength of fitness advantage compared to TP53 disruption.

By comparing tumor samples collected prior to treatment and after relapse, “we found that genomic evolution after therapy is the rule rather than the exception,” Wu said. “Certain mutations were present in a greater number of leukemia cells within a sample after relapse, showing that these mutations, presumably, allow the tumor to persevere.”

Researchers also discovered that several BRAF mutations occurred near but not at the spot most commonly involved in other cancers.

“This study also provides a vision of what the next phase of large scale genomic sequencing efforts may look like,” said first author Dan Landau MD, PhD, of Dana-Farber, the Broad Institute of MIT and Harvard, and Brigham and Women’s Hospital. “The growing sample size allows us to start engaging deeply with the complex interplay between different mutations found in any individual tumor, as well as reconstructs the evolutionary trajectories in which these mutations are acquired to allow the malignancy to thrive and overcome therapy.”

Landau DA, Tausch E, Taylor-Weiner AN, et al. Mutations driving CLL and their evolution in progression and relapse. Nature. 2015;526:525-530.