Researcher Ding Yi of the Basic Medical School, Associate Researcher Zhao Huaxiang of the Stomatological Hospital, Associate Researcher Yin Chunyan of the Second Affiliated Hospital, and Chief Physician Huang Huimei of the Affiliated Children's Hospital of Xi'an Jiaotong University (XJTU) published a research paper titled Exome sequencing reveals the genetic architecture of non-syndromic orofacial clefts and identifies BOC as a novel causal gene in the internationally renowned journal Advanced Science. The research was selected as the Frontispiece for high-profile recommendation in the issue.

Non-syndromic orofacial clefts (NSOCs) are the most common congenital developmental malformations in the oral and craniofacial region, affecting patients' appearance, oral and maxillofacial function, and mental health. The disease is caused by genetic factors, environmental factors, and their interaction. However, currently known pathogenic genes can only explain part of their genetic effect.

To further reveal the rare variant genetic architecture of NSOCs, the research team performed exome sequencing on 214 NSOC patients from western China, identifying a large number of candidate variants related to the occurrence of cleft lip and palate and providing a wealth of resources for future research, including 127 "pathogenic/possibly pathogenic" variants located in 80 genes - of which 11 are not included in the previously reported 418 cleft lip and palate genes (Diaz Perez et al., Genet Med, 2023).

Further bioinformatics analysis confirmed the allelic heterogeneity and genetic heterogeneity of NSOCs, and suggested that genetic variants affecting cleft lip and palate-related signaling pathways are more likely to be the pathogenic variants of cleft lip and palate and should be prioritized for functional verification.

The study further focused on three rare variants of the BOC gene and confirmed through in vitro cell experiments and in vivo zebrafish models that these variants are all loss-of-function variants.

More interestingly, in a pedigree exhibiting submucous cleft lip, the study found that patients in the family simultaneously carried a nonsense variant of BOC (p.R681X, a very strong loss-of-function variant) and an activating variant of GLI2 (p.A543G).

Subsequent functional mechanism studies found that the activating variant of GLI2 can partially offset the signal downregulation caused by BOC inactivation, explaining why patients carrying extremely destructive loss-of-function variants only exhibit a mild cleft lip phenotype.

Based on this, the research team proposed for the first time a "epistatic two-gene antagonistic genetic model" for NSOCs: two mutations in different genes produce antagonistic effects in the same signaling pathway, thereby jointly determining the final phenotype.

This mechanism is different from the traditional "digenic inheritance" model (i.e., two alleles synergistically causing the occurrence of disease) and provides a new genetic explanation framework for complex developmental diseases, including NSOCs.