A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and...

Area of Science:

• Genomics
• Cancer Biology
• Molecular Genetics

Background:

• Mutational signatures provide insights into the molecular mechanisms driving tumorigenesis.
• Understanding endogenous DNA damage repair is crucial for cancer research.

Purpose of the Study:

• To investigate the role of specific genes in mitigating endogenous DNA damage.
• To characterize the mutational signatures resulting from the deficiency of these genes.
• To develop a tool for detecting DNA repair deficiencies in cancer.

Main Methods:

• Generated CRISPR-Cas9 knockouts of 43 genes in human induced pluripotent stem cells.
• Performed whole-genome sequencing on 173 subclones.
• Developed and applied a classifier (MMRDetect) to whole-genome sequencing data from 7,695 cancers.

Main Results:

• Specific gene knockouts (e.g., OGG1, MLH1, MSH2) produced distinct mutational signatures.
• Revealed mechanistic insights into DNA repair pathways, including sequence-context specificity of 8-oxo-dG elimination.
• Identified distinct signatures for different mismatch repair gene deficiencies.
• MMRDetect classifier enhanced the detection of mismatch repair-deficient tumors.

Conclusions:

• Key genes play critical roles in mitigating endogenous DNA damage.
• Mutational signatures can elucidate complex DNA repair mechanisms.
• The MMRDetect classifier improves the identification of mismatch repair-deficient cancers, with potential implications for immunotherapy response.