By Richard Simoneaux



With roughly 60 percent of the disease risk being genetically determined, chronic lymphocytic leukemia (CLL) is one of the most inheritable malignancies. Although CLL is known to be heritable, little is known about the genetic variation which gives rise to CLL. Previous research has identified that rare germline variants of ATM (ataxia telangiectasia mutated), a gene that encodes a serine/threonine kinase that is involved in the repair of double-strand DNA breaks, as the first risk gene for CLL (Leukemia 2017;31:2244-2247). One of the co-leaders of that research was Jennifer R. Brown, MD, PhD, Director of the Chronic Lymphocytic Leukemia Center at Dana-Farber Cancer Institute. In a subsequent study being led by Brown, a deep learning-based germline variant calling algorithm is being utilized to analyze germline mutations in both DNA repair and cell cycle-associated genes to assess their relevance to CLL.

"Although our data are preliminary, it appears that those having germline mutations in at least certain genes associated with DNA repair may be at an increased risk for CLL," Brown noted. The findings from this study were presented at the 2019 ASCO Annual Meeting.

Study Methods

"This study, which was a two-stage, case-control analysis, was performed using a gene-based mutational enrichment analysis of 50 established cancer predisposition DNA repair and cell cycle genes," Brown explained.

For the first part of the study, or discovery phase, analysis was performed on a cohort of 569 European (non-Finnish) CLL patients and 8,608 ancestry-matched, cancer-free controls. A false discovery rate correction was applied with genes having a q-value < 0.1 in both cohorts being deemed statistically significant.

For the second part of the study, or validation phase, which is still ongoing, 314 Spanish patients with CLL were analyzed with the appropriately ancestry-matched control cohort still pending analysis. This analysis focused only on high functional impact mutations, for example frameshift or nonsense mutations.

Results

Pathogenic variants of CHEK2, a tumor suppression gene that encodes the serine/threonine kinase CHK2, were found to be more prevalent in patients with CLL relative to ancestry-matched controls. The known founder CHEK2 loss of function (LOF) 1100delC variant was independently enriched in CLL patients relative to controls, with an odds ratio (OR) of 6.5 (95%CI: 2.1-18.2, p=0.001). However, significant enrichment in CHEK2 LOF variants persists, even after removal of 1100delC, with an OR of 2.9 (95%CI: 1.3-6.1, p=0.0070). In addition, the low-penetrance allele c.599T>C variant CHEK2 is enriched in CLL patients versus controls, with an OR of 7.7 (95%CI: 3.6-15.6).

Discussion

"From our analyses, we identified CHEK2 as a novel gene, which if mutated, may potentially predispose patients to develop CLL," Brown stated. "The identification of this gene may further add to the evidence that genes involved in the DNA repair and cell cycle regulation pathways could be potentially important drivers of CLL susceptibility." The serine/threonine kinase CHK2, which regulates cell division, is activated by double strand DNA breaks.

When asked to describe their methods for identifying mutations, Brown elaborated, "We leveraged sequencing technology to look for rare variations (i.e., those that are present in less than 1 percent of the population) and assessed their enrichment among CLL cases compared to ancestry-matched cancer-free controls. In these studies, we only looked at germline mutations; we did not evaluate somatic mutations, although, looking at associations of somatic mutations with the germline mutations, we have found, is of interest for further work."

In discussing future directions for this research, Brown noted, "We will likely want to expand the search to other potentially pathogenic germline variants, such as missense mutations, in the DNA repair and cell cycle control pathways, and to expand analyses of both high impact and missense mutations, to explore the entire exome. This would likely necessitate an increase in the size of the cohorts in order to increase our power for finding rare variants."

Richard Simoneaux is a contributing writer.



