Knocking-out the human face genes TBX15 and PAX1 in mice alters facial and other physical morphology

DNA variants in or closed to the human TBX15 and PAX1 genes have been repeatedly associated with facial morphology in independent genome-wide association studies, while their functional roles in determining facial morphology remains to be understood. We generated Tbx15 knockout ( Tbx15-/- ) and Pax1 knockout ( Pax1-/- ) mice by applying the one-step CRISPR/Cas9 method. A total of 75 adult mice were used for subsequent phenotype analysis, including 38 Tbx15 mice (10 homozygous Tbx15-/- , 18 heterozygous Tbx15 +/-, 10 wild-type WT) and 37 Pax1 mice (12 homozygous Pax1-/- , 15 heterozygous Pax1 +/-, 10 WT mice). Facial and other physical morphological phenotypes were obtained from three-dimensional (3D) images acquired with the HandySCAN BLACK scanner. Compared to WT mice, the Tbx15-/- mutant mice had significantly shorter faces ( P =1.08E-8, R2=0.61) and their ears were in a significantly lower position ( P =3.54E-8, R2=0.62) manifesting an “ear dropping” characteristic. Besides these face alternations, Tbx15-/- mutant mice displayed significantly lower weight as well as shorter body and limb length. Pax1-/- mutant mice showed significantly longer noses ( P =1.14E-5, R2=0.46) relative to WT mice, but otherwise displayed less obvious morphological alterations than Tbx15-/- mutant mice did. Because the Tbx15 and Pax1 effects on facial morphology we revealed here in mice are largely consistent with previously reported TBX15 and PAX1 face associations in humans, we suggest that the functional role these two genes play on determining the face of mice is similar to the functional impact their human homologues have on the face of humans. Author Summary Several independent genome-wide association studies (GWASs) on human facial morphology highlighted DNA variants in or closed to TBX15 and PAX1 with genome-wide significant association with human facial phenotypes. However, direct evidence on the functional involvement if these genes in the development and determination of facial morphology has not been established as of yet. In the current study, our in vivo gene editing experiments in mice for two well-replicated human face TBX15 and PAX1 genes provide novel evidence on the functional involvement of these two genes in facial and other physical morphology in mice, at least. Tbx15-/- mice showed a shortened facial length and manifesting an ear dropping characteristic, Pax1-/- mice showed an increased nose length. Our geometric morphometrics analysis further indicate that there are significant facial morphology differences between groups ( Tbx15-/- and Tbx15+/-, Tbx15-/- and Tbx15+/+, Tbx15+/- and Tbx15+/+, Pax1-/- and Pax1+/+ ). We provide the first direct functional evidence that two well-known and replicated human face genes, Tbx15 and Pax1 , impact facial and other body morphology in mice. The general agreement between our findings in knock-out mice with those from previous GWASs suggests that the functional evidence we established here in mice may also be relevant in humans. ### Competing Interest Statement The authors have declared no competing interest.