Sensitive detection of Cre-mediated recombination using droplet digital PCR reveals Tg(BGLAP-Cre) and Tg(DMP1-Cre) are active in multiple non-skeletal tissues

In humans, somatic activating mutations in PIK3CA are associated with skeletal overgrowth. In order to determine if activated PI3K signaling in bone cells causes overgrowth, we used Tg(BGLAP-Cre) and Tg(DMP1-Cre) mouse strains to somatically activate a disease-causing conditional Pik3ca allele (Pik3ca(H1047R)) in osteoblasts and osteocytes. We observed Tg(BGLAP-Cre);Pik3ca(H1047R/+) offspring were born at the expected Mendelian frequency. However, these mice developed cutaneous lymphatic malformations and died before 7 weeks of age. In contrast, Tg(DMP1-Cre);Pik3ca(H1047R/+) offspring survived and had no cutaneous lymphatic malformations. Assuming that Cre-activity outside of the skeletal system accounted for the difference in phenotype between Tg (BGLAP-Cre);Pik3ca(H1047R/+) and Tg(DMP1-Cre);Pik3ca(H1047R/+) mice, we developed sensitive and specific droplet digital PCR (ddPCR) assays to search for and quantify rates of Tg(BGLAP-Cre)- and Tg(DMP1-Cre)-mediated recombination in non-skeletal tissues. We observed Tg(BGLAP-Cre)-mediated recombination in several tissues including skin, muscle, artery, and brain; two CNS locations, hippocampus and cerebellum, exhibited Cre-mediated recombination in > 5% of cells. Tg(DMP1-Cre)-mediated recombination was also observed in muscle, artery, and brain. Although we cannot preclude that differences in phenotype between mice with Tg(BGLAP-Cre)- and Tg(DMP1-Cre)-mediated PIK3CA activation are due to Cre-recombination being induced at different stages of osteoblast differentiation, differences in recombination at non-skeletal sites are the more likely explanation. Since unanticipated sites of recombination can affect the interpretation of data from experiments involving conditional alleles, we recommend ddPCR as a good first step for assessing efficiency, leakiness, and off-targeting in experiments that employ Cre-mediated or Flp-mediated recombination.

Automated summary

In this study, the researchers investigated the effects of somatic activating mutations in the PIK3CA gene on skeletal overgrowth in mice. They found that differences in phenotype between Tg(BGLAP-Cre) and Tg(DMP1-Cre) mice with PIK3CA activation may be attributed to differences in recombination rates at non-skeletal sites outside of the bone system. The development of droplet digital PCR assays allowed for the detection and quantification of recombination efficiency in various tissues, providing insights into the potential impact of off-targeting in experiments involving conditional alleles.