Data from Functional Analysis Identifies Damaging CHEK2 Missense Variants Associated with Increased Cancer Risk
Abstract
Abstract Heterozygous carriers of germline loss-of-function variants in the tumor suppressor gene checkpoint kinase 2 (CHEK2) are at an increased risk for developing breast and other cancers. While truncating variants in CHEK2 are known to be pathogenic, the interpretation of missense variants of uncertain significance (VUS) is challenging. Consequently, many VUS remain unclassified both functionally and clinically. Here we describe a mouse embryonic stem (mES) cell–based system to quantitatively determine the functional impact of 50 missense VUS in human CHEK2. By assessing the activity of human CHK2 to phosphorylate one of its main targets, Kap1, in Chek2 knockout mES cells, 31 missense VUS in CHEK2 were found to impair protein function to a similar extent as truncating variants, while 9 CHEK2 missense VUS resulted in intermediate functional defects. Mechanistically, most VUS impaired CHK2 kinase function by causing protein instability or by impairing activation through (auto)phosphorylation. Quantitative results showed that the degree of CHK2 kinase dysfunction correlates with an increased risk for breast cancer. Both damaging CHEK2 variants as a group [OR 2.23; 95% confidence interval (CI), 1.62–3.07; P < 0.0001] and intermediate variants (OR 1.63; 95% CI, 1.21–2.20; P = 0.0014) were associated with an increased breast cancer risk, while functional variants did not show this association (OR 1.13; 95% CI, 0.87–1.46; P = 0.378). Finally, a damaging VUS in CHEK2, c.486A>G/p.D162G, was also identified, which cosegregated with familial prostate cancer. Altogether, these functional assays efficiently and reliably identified VUS in CHEK2 that associate with cancer. Significance: Quantitative assessment of the functional consequences of CHEK2 variants of uncertain significance identifies damaging variants associated with increased cancer risk, which may aid in the clinical management of patients and carriers.
Authors 16
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Leiden University Medical Center
Affiliation as printed
Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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Radboud University Nijmegen · Radboud University Medical Center · Bio-Prodict (Netherlands)
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Bio-Prodict, Nijmegen, the Netherlands
Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center, Nijmegen, the Netherlands
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Affiliation as printed
Bio-Prodict, Nijmegen, the Netherlands
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Affiliation as printed
The Institute of Cancer Research, London, United Kingdom
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Institute of Cancer Research · Illumina (United Kingdom)
Affiliation as printed
Illumina Cambridge Ltd., Cambridge, United Kingdom
The Institute of Cancer Research, London, United Kingdom
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SIB Swiss Institute of Bioinformatics · ETH Zurich
Affiliation as printed
ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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Leiden University Medical Center
Affiliation as printed
Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
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SIB Swiss Institute of Bioinformatics · ETH Zurich
Affiliation as printed
ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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Affiliation as printed
The Institute of Cancer Research, London, United Kingdom
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Peter Devilee Aachen Department of Human Genetics Department of Pathology, Leiden University Medical Center
Leiden University Medical Center
Affiliation as printed
Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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Affiliation as printed
Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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Leiden University Medical Center
Affiliation as printed
Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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