A missense variant effect map for the human tumor-suppressor protein CHK2

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.