Knocking Out Assumptions: Hidden Challenges in Transgenic Mouse Models

When researchers from the Duchêne Lab  first analyzed the transcriptome of the widely used ACKR1 knockout mouse model, they were excited by the large changes observed—until they discovered that many altered genes clustered in the same genetic region. Their new study, led by Dr. Johan Duchêne and PhD student Zoe Möller Ramon, with Professor Antal Rot from Queen Mary University, London, reveals that "passenger mutations"—genetic variations originating from the original donor strain—can significantly impact the interpretation of gene function in knockout models, potentially leading to misleading conclusions.

The study specifically examined ACKR1-deficient mice, and showed that genetic remnants from the original donor strain affected the expression of immune-related genes. By mapping gene activity across different cell type, the team identified substantial differences in immune gene expression that were not due to the targeted gene knockout itself but rather to these background mutations.

This discovery challenges the conventional use of standard knockout models in preclinical studies, where such background genetic effects are often overlooked. The findings suggest that researchers must account for these passenger mutations or use alternative approaches to better study the gene of interest, such as conditionally genetically modified mouse models or  CRISPR CAS9 gene editing technology. This refinement could significantly improve the accuracy and reproducibility of genetic studies.

Johan Duchêne who is also a member of the interdisciplinary LMU Open Science Center emphasized, "Our work underscores the importance of recognizing the limitations of traditional knockout models and exploring more precise tools in genetic research."

The publication aims to spark a broader conversation about the use of genetic models in biomedical research and encourages the adoption of methods that can minimize background noise in experimental results.