Comprehensive RNA and protein functional assessments contribute to the clinical interpretation of MSH2 variants...

Area of Science:

• Genetics and Molecular Biology
• Cancer Genomics
• DNA Repair Mechanisms

Background:

• Spliceogenic variants are often assumed pathogenic due to frameshifts causing loss of function.
• However, some variants in cancer predisposition genes can cause in-frame anomalies that preserve protein function.
• The MSH2 gene, crucial for DNA mismatch repair and implicated in Lynch syndrome, was used as a model to investigate this phenomenon.

Purpose of the Study:

• To determine if in-frame spliceogenic variants in the MSH2 gene lead to loss of function.
• To assess the pathogenicity of these variants in the context of Lynch syndrome.
• To highlight the importance of integrated RNA and protein analysis for variant interpretation.

Main Methods:

• Minigene splicing assays were employed to analyze 18 MSH2 variants, primarily at canonical splice sites.
• The functional impact of resulting protein alterations was evaluated using a methylation tolerance-based assay.
• Clinicopathological data from variant carriers were collected and correlated with molecular findings.

Main Results:

• Three types of in-frame RNA biotypes were identified: exon skipping, segmental exonic deletions, and intronic retentions.
• The 10 resulting protein isoforms exhibited deletions or insertions, ranging from 12 to 93 amino acids.
• All analyzed MSH2 variants abrogated protein function, consistent with the clinical presentation of variant carriers.

Conclusions:

• MSH2 function is highly sensitive to in-frame indels induced by spliceogenic variants, supporting their pathogenic role in Lynch syndrome.
• These findings underscore the necessity of combining RNA and protein analyses for precise clinical interpretation of in-frame spliceogenic variants.
• Accurate interpretation is crucial for diagnosing and managing Lynch syndrome patients.