Quantitative evaluation of incomplete preweaning lethality in mice by using the CRISPR/Cas9 system

Area of Science:

• Genetics
• Developmental Biology
• Genomics

Background:

• Genome editing enables creation of mouse mutants for most genes, leading to databases like the International Mouse Phenotyping Consortium (IMPC).
• Preweaning lethality is a critical phenotype for assessing gene essentiality, but survival rates in homozygous knockout mice are highly variable.
• Existing data on incomplete lethality in the IMPC database lacks a standardized quantitative measure.

Purpose of the Study:

• To propose and validate a simple quantitative indicator, the lethal allele index (LAI), for preweaning lethality in genome-edited mice.
• To assess the correlation of LAI with gene disease relevance and human loss-of-function allele frequencies.
• To evaluate the utility of LAI in CRISPR/Cas9-generated mouse models.

Main Methods:

• Calculated the lethal allele index (LAI) as the ratio of observed to theoretically predicted homozygous knockout mice.
• Analyzed IMPC data for mouse mutants registered with incomplete preweaning lethality.
• Utilized CRISPR/Cas9 to edit the Ehd1 gene in cell lines and mice, analyzing genotype distributions and calculating LAI.

Main Results:

• The LAI was lower for disease-related genes among IMPC incompletely lethal mutants and correlated with human loss-of-function allele frequencies.
• In CRISPR/Cas9-edited mice, homozygous frameshift alleles appeared associated with lethality.
• LAI calculated from Ehd1 gene editing in mice aligned with IMPC data, supporting its validity.

Conclusions:

• The lethal allele index (LAI) serves as a useful quantitative measure for preweaning lethality in genome-edited mice.
• LAI can help prioritize genes for further study based on their essentiality for survival.
• The LAI framework is applicable to mouse models generated using various genome editing technologies, including CRISPR/Cas9.