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Published on: April 4, 2018
A missense variant effect map for the human tumor-suppressor protein CHK2
Marinella Gebbia1, Daniel Zimmerman1, Rosanna Jiang1
1The Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.
Abstract:
The tumor suppressor CHEK2 encodes the serine/threonine protein kinase CHK2 which, upon DNA damage, is important for pausing the cell cycle, initiating DNA repair, and inducing apoptosis. CHK2 phosphorylation of the tumor suppressor BRCA1 is also important for mitotic spindle assembly and chromosomal stability. Consistent with its cell-cycle checkpoint role, both germline and somatic variants in CHEK2 have been linked to breast and other cancers. Over 90% of clinical germline CHEK2 missense variants are classified as variants of uncertain significance, complicating diagnosis of CHK2-dependent cancer. We therefore sought to test the functional impact of all possible missense variants in CHK2. Using a scalable multiplexed assay based on the ability of human CHK2 to complement DNA sensitivity of Saccharomyces cerevisiae cells lacking the CHEK2 ortholog, RAD53, we generated a systematic "missense variant effect map" for CHEK2 missense variation. The map reflects known biochemical features of CHK2 while offering new biological insights. It also provides strong evidence toward pathogenicity for some clinical missense variants and supporting evidence toward benignity for others. Overall, this comprehensive missense variant effect map contributes to understanding of both known and yet-to-be-observed CHK2 variants.
Insights
This study maps the functional impact of all CHEK2 missense variants, aiding cancer diagnosis. The findings clarify the pathogenicity of CHEK2 variants, improving understanding of CHEK2-dependent cancers.
Area of Science:
- Genetics
- Molecular Biology
- Cancer Research
Background:
- The CHEK2 gene encodes the CHK2 protein kinase, crucial for DNA damage response, cell cycle control, and apoptosis.
- CHEK2 also phosphorylates BRCA1, impacting mitotic spindle assembly and chromosomal stability.
- Germline and somatic CHEK2 variants are associated with various cancers, but most clinical missense variants are of uncertain significance.
Purpose of the Study:
- To systematically assess the functional impact of all possible missense variants in the CHEK2 gene.
- To create a comprehensive missense variant effect map for CHEK2.
- To aid in the clinical diagnosis of CHEK2-dependent cancers by clarifying variant pathogenicity.
Main Methods:
- A scalable multiplexed assay was developed using Saccharomyces cerevisiae cells lacking the CHEK2 ortholog, RAD53.
- Human CHK2 variants were tested for their ability to complement the DNA sensitivity of these yeast cells.
- A systematic missense variant effect map for CHEK2 was generated based on functional complementation data.
Main Results:
- The generated missense variant effect map reflects known biochemical properties of CHK2 and provides new biological insights.
- The map offers strong evidence for the pathogenicity of some clinical CHEK2 missense variants.
- Supporting evidence for the benign nature of other clinical CHEK2 missense variants was also provided.
Conclusions:
- This comprehensive missense variant effect map significantly contributes to understanding CHEK2 function and variation.
- The findings help in classifying the clinical significance of both known and novel CHEK2 variants.
- This work supports improved diagnosis and management of CHEK2-related cancers.
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