DNA Methylation’s Role in Preventing Cleft Lip and Palate

Cleft lip and palate stand out as the most prevalent craniofacial birth anomalies worldwide, affecting approximately 1 in 700 newborns. Despite extensive research spanning decades, the precise etiology of most cases remains elusive, as does effective preventive measures.

Understanding the causes of this abnormality has mainly focused on genetic factors, revealing numerous risk loci along the DNA, although direct causative variants are rare. Therefore, it is thought that this defect arises from a mix of genetic and environmental factors. Yet, the precise environmental triggers and mechanisms remain unclear.

In a recent investigation conducted at the University of Wisconsin (UW) School of Veterinary Medicine, researchers studying orofacial development in mice are shedding light on the development of cleft lip and palate, potentially paving the way for mitigating the incidence of these defects in humans. Published in the Proceedings of the National Academy of Sciences (PNAS), the study unveils direct evidence of DNA methylation’s pivotal role in craniofacial development.

DNA methylation is an epigenetic process that involves the addition of methyl groups to DNA molecules, usually at specific locations known as CpG sites. This modification doesn’t alter the DNA sequence itself but can influence gene expression, impacting various biological functions. Responsive to environmental factors, DNA methylation further contributes to its regulatory role in gene activity. In this study, the researchers found that changes in DNA methylation affect the development of the lip and palate, leading to these types of congenital disabilities.

Under the leadership of Robert Lipinski, associate professor of comparative biosciences at UW School of Veterinary Medicine, this research marks a significant stride towards formulating preventive strategies to mitigate the risk of cleft lip and palate, collectively referred to as orofacial clefts (OFCs), in both animals and humans.

“We knew from past research that genetics and the environment interact to cause these types of birth defects,” said Lipinski, “but our understanding of the environmental component lagged far behind that of genetics.” 

He emphasized that, unlike genetics, there isn’t a permanent record of the prenatal environment for retrospective examination. However, linking OFCs to DNA methylation helps us narrow our focus on specific environmental influences that contribute to the risk of these birth defects.

In previous articles, we have discussed how inherited epigenetic marks can influence embryo development. We also discussed how the prenatal environment affects offspring development. DNA methylation was analyzed in both studies to determine the environment’s influence on phenotype

Here, the team’s findings underscore the critical role of DNA methylation in orchestrating orofacial development during embryonic stages and elucidate how disruptions to this process impair stem cells’ capacity to form craniofacial bone and cartilage, precipitating OFCs.

The researchers manipulated DNA methylation genetically in two distinct sets of mouse embryos, yielding apparently conflicting outcomes—OFCs in one group but not in the other.

To comprehend this disparity, the team conducted further experiments inhibiting DNA methylation in mouse embryos at various developmental stages, revealing the timing’s crucial significance. Exposure on the 10th gestational day resulted in OFCs, whereas the same inhibition administered just 48 hours later led to normal orofacial development.

Identifying this narrow gestational window is crucial, Lipinski notes, as it guides the next stage of research focus and informs future public education initiatives about modifiable environmental and behavioral risk factors impacting OFC risk in humans. This sensitive period, occurring around the 10th gestational day in mouse embryos, aligns with the 5th week of embryonic development in humans, often before pregnancies are recognized.

“We know DNA methylation can be influenced by a variety of environmental factors, including maternal stress, diet, and exposure to drugs, toxins, and environmental pollutants, and having a better understanding of how orofacial development is regulated by environmentally sensitive mechanisms could directly inform birth defect prevention strategies,” Lipinski states.

In the upcoming phase, the research team will concentrate on identifying particular factors that influence DNA methylation during orofacial development, potentially altering OFC risk. Moreover, the team’s development of a new in vitro model facilitates rapid screening of numerous dietary and environmental factors in a controlled setting before testing their impact on cleft susceptibility in mouse models.

Insights gained from cell and animal models are anticipated to expedite the identification of factors pertinent to human development.

Source: Caden M. Ulschmid et alDisruption of DNA methylation–mediated cranial neural crest proliferation and differentiation causes orofacial clefts in mice. January 9, 2024.

Reference: Gian Galassi UW researchers uncover new clues about the cause of common birth defects. University of Wisconsin-Madison. January 22, 2024.

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