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Exome Sequencing of CLL Uncovers Driver Genes Involved in Progression, Relapse

NEW YORK (GenomeWeb) – By sequencing the exomes of chronic lymphocytic leukemia, researchers from the Broad Institute and the Dana-Farber Cancer Institute have homed in on mutations that appear to drive the disease.

The Broad's Catherine Wu and her colleagues detected 44 putative CLL driver genes from within their cohort of some 500 CLL and matched germline samples, as they reported today in Nature. These potential driver genes also highlighted signaling pathways affected in the disease. The researchers further began to untangle the order in which these mutations crop up and spied differences in the mutations present in pre-treatment and relapse samples.

"Sequencing the DNA of CLL has taught us a great deal about the genetic basis of the disease," Wu said in a statement.

The researchers sequenced the exomes of CLL and matched germline samples from 278 research participants enrolled in the phase III CLL8 trial to a mean read-depth of 95 and 95.7, respectively. Using MutSig2CV, they inferred candidate cancer-associated genes in CLL.

To boost their detection capabilities, the researchers folded in data from two additional, non-overlapping exome studies of CLL, bringing their cohort size to 538.

From this dataset, they uncovered 44 putative CLL driver genes, including 18 previously identified drivers. About a third of the samples, they noted, had a mutation in at least one of the 26 other genes.

Some of these putative driver genes had been previously linked to CLL. For instance, MGA, a MYC suppressor, which was recurrently inactivated in this set of samples by insertion and nonsense mutations, had been found to be inactivated in high risk-CLL due to deletions and truncating mutations.

Two other candidate genes the researchers identified — PTPN11 and FUBP1 — also likely modulate MYC activity.

These novel CLL drivers also affected other pathways. Wu and her colleagues reported that nearly 9 percent of patients had at least one mutation affecting the MAPK-ERK pathway, including in RAS, KRAS, BRAF, or MAP2K1 genes. The researchers thus suggested that a therapeutic exploration of this pathway might be beneficial.

Other pathways and processes like RNA processing and export, DNA damage, chromatin modification, and B cell activity-related pathways were also affected by these novel CLL drivers.

Some putative driver genes had never before been linked to cancer in humans, including the RPS15 gene, which was mutated in 4.3 percent of CLLs, and IKZF3, which was mutated in 2 percent of CLLs.

Some of these drivers, the researchers added, appeared to influence clinical outcomes. Shorter progression-free survival, they said, was linked with TP53 and SF3B1 mutations, as well as with the newly identified recurrent mutations in RPS15.

Wu and her colleagues also found that some mutations were more likely to occur in concert with certain other ones. TP53 mutations and del(17p) were likely to co-occur, as were ATM mutations and del(11q), they reported. At the same time, there was a low rate of co-occurrence between del(13q) and tri(12).

In addition, they noted that the IGHV-mutated subtype of CLL was enriched for three driver genes: del(13q), YD88, and CHD2.

By determining the cancer-cell fraction of each mutation across the sample set, the researchers began to piece together the order in which mutations occur in CLL. The earliest events, they reported, typically involve copy-number alterations at del(13q) or tri(12), as well as an early convergence toward del(11q).

For a subset of CLL cases, the researchers also sequenced samples from the time of disease relapse, noting a large clonal shift between the two time periods. In nearly a third of cases, the relapse clone was detectable in the pre-treatment CLL.

By comparing the pre-treatment and relapse cancer-cell fraction for each driver, the researchers found that the early drivers of del(11q), del(13q), and tri(12) were stably clonal, despite marked evolution, confirming to the researchers that these were early events likely shared by CLL cells.

In addition, they noted an increase of TP53 mutations and del(17p) upon relapse, which could indicate a fitness advantage under therapeutic selection. The newly identified IKZF3 mutation also increased in a portion of relapse cases.

"The detailed characterization of the compendium of driver lesions in cancer is of particular importance as we strive to develop personalized medicine, because driver genes may inform prognosis … and identify lesions that may be targeted by therapeutic intervention," Wu and her colleagues noted in their paper.

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