HMN 2025: How to Uncover the why behind cleft lip and palate with live imaging and gene editing

Every face is unique. Genetics helps to determine our features, but sometimes genes have errors which, in early fetal development, can result in babies with facial differences such as a cleft lip or cleft palate. If not treated, these craniofacial conditions can have a major impact on a baby’s quality of life by interfering with a baby’s ability to see, breathe, speak clearly, and avoid ear infections.

In his lab, UC San Francisco Professor Jeffrey Bush, Ph.D., examines how the human face forms in utero. Bush studies craniofacial birth defects of many kinds, including malformed or underdeveloped facial bones, cheekbones, and jaws, as well as two of the most common birth defects, cleft lip and cleft palate.

“Craniofacial birth defects are a class of disease where we don’t have a single medicine to treat the conditions,” said Bush, chair of the School of Dentistry’s Department of Cell and Tissue Biology.

“The general approach to treating these conditions is for the infant to undergo multiple surgeries after birth, but there is no current preventive treatment in utero. Understanding how development happens is a necessary first step to figuring out non-surgical treatments for these infants.”

Uncovering the ‘why’ behind birth defects

One in 33 babies is born with a structural difference, ranging from heart defects to facial malformations, according to the Centers for Disease Control and Prevention (CDC). Of those, about one in 700 are born with cleft lip or cleft palate, making these conditions the fourth most common birth defects in the U.S.

A cleft lip is a separation of the two sides of the lip, usually involving the bones of the upper jaw, upper gum, or both. A cleft palate is an opening in the roof of the mouth, sometimes running from the front teeth to the throat, in which the tissue on the two sides of the palate didn’t fuse properly.

The anomalies are apparent at birth and can be detected in ultrasounds during pregnancy, so most parents opt for surgeries early in their child’s life to correct the irregularities while their child’s bones are pliable and growing. Depending on the severity of the condition, this can result in numerous surgeries during the child’s early years.

Bush and his team of graduate students, postdoctoral learners, and staff study the cellular and molecular steps that occur in the embryo to form the human face. Using advanced microscopes, they’ve filmed mouse embryos to observe how tiny facial structures grow, move, and fuse or “zip” together—a process that, when it fails, can cause cleft lip or palate.

At a cellular level, they have identified how genes influence embryo facial development in mouse models, which mimic that of humans. Their hope is that identifying these early processes in fetal development and understanding how they interact with environmental factors, like nutrition and smoking, will help to identify when and how things go wrong.

Using CRISPR gene-editing tools, they recreate gene changes seen in human patients and observe how they affect the formation of the face. This research helps scientists see what happens when the “zipper” doesn’t close correctly.

The first time-lapse of tissues fusing

A major breakthrough, led by the Bush lab and published in the Journal of Cell Biology, was achieved by using new live-imaging techniques to observe lip development in real time. Together with CRISPR-Cas9 gene editing approaches, this work led to the discovery of a network of cell-to-cell adhesion and tiny cell movements that prompt the tissue on two sides of the developing upper lip to fuse together. Identifying this network was a step forward.

Further examination identified that a gene called CDH3 provides instructions for making a protein that helps cells stick to each other and is vital for tissue development. Disruption of this gene may play a role in causing cleft lip in humans.

“Our goal was to understand the cell biology of tissue fusion, which is a crucial process in the development of the face,” Bush said. “We wanted to understand how cells move, and how they generate forces to drive two separate embryonic tissues to fuse together. These results were a breakthrough toward understanding that process.”

Postdoctoral researcher Camilla Teng was the first author of the recently published study. Driven by a curiosity to understand the development of the human face and skull, Teng’s interests dovetailed beautifully with Bush’s work, and she has been a member of the lab team for about six years.

Teng combined her interest in how tissues take shape with her interest in microscopic imaging to create a time-lapse video, comprised of snapshots taken every 15–20 minutes of the lip fusion process in mouse embryos.

“I’m very fortunate to have learned gene editing and live imaging techniques used at this lab to identify the specific function of proteins that enables tissue fusion to form the lips,” Teng said. “I think this work was powerful in determining the function of multiple cellular mechanisms in this process.”

And one of the best things about their breakthrough is that tracking and dissecting proteins that cause these mutations is applicable to many diseases and medical disorders.

“Adult diseases, such as cancer, involve the same genes that are important during facial development,” Bush said. “So, understanding fundamentally what these genes do in development is extremely useful for understanding all human diseases and for regenerative biology approaches to treat them.”

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