Genes directly related to cleft lip and palate

Researchers are discovering more genes
directly related to cleft lip and palate.

In a new study, a team led by the University of Iowa determined that the deletion of three genes causes cleft lip and palate, and according to the Centers for Disease Control and Prevention, one in every 1,600 babies born in the United States will develop facial deformation
.

The team identified these genes through a high-resolution search of the genomes of more than 1,000 patients with cleft lip and palate, the result of
Iowa's longstanding involvement in global research on cleft lip or palate disease.

Cleft lip and palate are birth defects
that occur when a baby's lips or mouth do not form properly during pregnancy.
Children with cleft lip and palate often have problems eating and speaking clearly, and may develop ear infections
.

In patients with the disease, researchers found that a small portion of the genome was deleted or duplicated, called copy number variation
.
In the deleted section, the researchers looked for genes
that are rare even in people with the disease.
This is important because by looking for gene losses that are rare in people with the disease — and even rarer or absent in others — it means that these losses should play a central role in division, not just causing the disease
.

The researchers then confirmed a direct link
between these genes and cleft lip and palate by reducing the gene function of two species, the African clawed frog and the zebrafish.
When the function of the target gene decreased, each species showed signs of
division.

"We have discovered and validated three genes directly related to this disease in vertebrate experiments," said
John Manak, a professor in the Department of Biology at the University of Iowa and corresponding author of the study.
"It's still a long time before we can take action in humans, but now we've added several key genes
that drive the disease.
" Ultimately, if you know the genes behind cleft lip and palate, and the step-by-step process of how to build a face, then you might know how to intervene to prevent the defect.

”

The cause of cleft lip and palate in most babies is unknown, but it is thought to be caused by genetic changes or external factors
.

The researchers analyzed the DNA
of patients with cleft lip in the United States and the Philippines.
The large patient population is provided by Jeffrey Murray, a professor of pediatrics at the Stead Family in Iowa; Sandra Daack-Hirsch, professor in the School of Nursing; And many others, who have traveled to the Philippines for years to recruit patients with cleft lip and palate and their families to collect samples and information about the disease as part of
an Operation Smile-sponsored surgical mission.

"The families who generously participated in this study hope that this work will one day improve the prevention or treatment of cleft lip and palate, and this work is a milestone step
in that direction," Murray said.

From the DNA of these patients, Manak used a technique called comparative genomic hybridization, looking for deleted DNA fragments in patients with the disease and comparing
them to a control group that did not show cracks.
On this basis, he tried to find deletions that were very rare in the split group, and less than 1% of the 1102 patients surveyed had these genes
.

Manak, a member of the Stade Family Pediatrics and Interdisciplinary Genetics graduate program in Iowa, said, "I wanted to identify those extremely rare mutations that cause this disease because harmful mutations are less frequent in the population
.
In other words, copy number loss, all you need is a gene deletion, and you get the disease
.
This is exciting because it defines some really critical genes
in the division pathway.
Of course, before we can be fully confident in the results, we also need to verify that our candidate genes are actually expressed in the face and meaningful
in participating in craniofacial development.
”

The researchers used this analysis to find three genes: COBLL1, RIC1 and ARHGEF38
.

When the team reduced the function of these genes in the African clawed frog and zebrafish embryos, each species showed signs of
altered facial development.
The experiments with frogs are particularly important because they evolved closer to humans than zebrafish, and experiments with frogs produced facial features
similar to those of human cleft lips and palates.

Lisa Lansdon, who received her PhD in genetics from Iowa in 2018 and is the first author of the study, said the study was the main focus of
her paper.
She also supervised a group of undergraduates who helped with the analysis
.

"When we test it in fish and frogs, it's very exciting to see this research evolve from the early design phase to the eventual discovery of new genes important for craniofacial development.
"

The findings build on a previous study published by Manak in 2018 in which he used the same genetic search technique in a small group of cleft lip and palate patients to find a gene directly related to cleft lip and palate, called ISM1
.
He verified the gene's role in division in experiments with clawed frogs, as in this study
.

"A bright spot for me is the strategy we used in both studies, looking for gene deletions that were rare in our disease cohort and even rarer or absent in our control group, which people often didn't think of
.
" It's much
easier to sequence genes and then look for more traditional mutations that alter gene function.
”

He's also excited because these genes may be important
in facial development.

"There are multiple pathways, genes, and interactions between many different cell types, so we need to identify all of these components to understand how a face fits together
," Manak said.