Analysis of genetic factors contributing to cleft lip and palate

Cleft lip and palate, which are mainly caused by genetic reasons, are two of the most common congenital malformations. It is still unknown which genes are exactly affected.

Now, a study headed by the University of Bonn has revealed new correlations: New mutations around familiar genes, like SPRY1, can contribute to the rise in the risk of the disease. Also, there is proof that the transcription factor Musculin is involved causally. The findings have now been reported online in the journal Human Genetics and Genomics Advances.

In the cleft lip and palate, the development of the mouth area is impaired in embryonic development. Until today, over 45 genetic segments have been known to comprise common risk variants.

We now also found an enrichment of rare variants, especially new mutations, at two of these regions.”

Dr Kerstin U. Ludwig, Head, Emmy Noether Group, Institute of Human Genetics, University Hospital Bonn

Furthermore, the researchers employed novel data examination methods to look for proof that the transcription factor Musculin also serves a role.

This suggests an involvement of embryonic development of facial muscles in cleft lip and palate. This had previously been suspected, but not yet demonstrated.”

Hanna Zieger, Study Lead Author and Ludwig’s Team Member, University of Bonn

Several genetic studies concentrate mostly on the areas of the genome that comprises the code for producing proteins. "We combined different approaches to interpret rare variants in the 98 percent that do not directly encode proteins," Ludwig says.

One of these methods focuses on those areas of the genome to which transcription factors can bind. These are proteins that identify certain base sequences of DNA, dock to them, and eventually impact the readout of nearby genes. Musculin is one such transcription factor.

Zieger, using her uniquely customized evaluation methods, could demonstrate that the base sequence of the binding sites of Musculin is modified more frequently and profoundly in patients in comparison to the control group. “The evaluation script written by Ms Zieger can also be used for other diseases,” adds Ludwig, who is a member of the Cluster of Excellence ImmunoSensation2.

Like a needle in a haystack

The team made use of publicly accessible genome-sequencing data available from the Gabriella Miller Kids First program of over 200 children with cleft lip and palate and their parents. Along with the Berlin Institute of Health and the Max Delbrück Center for Molecular Medicine (Berlin), the scientists filtered out genetic variants that happen only in the children who are affected but not in their parents.

Above 13,000 of such “new mutations” were gathered this way. The scientists equated these with nearly 17,000 new mutations from families that did not have this condition.

Now, the objective was to find such new mutations in patients with cleft lip and palate that were considerably more common in the patients rather than the control subjects.

This way, we were able to identify a section on chromosome 4. This section is close to the SPRY1 gene, which was already known to be a gene for cleft lip and palate due to common variants.”

Dr Kerstin U. Ludwig, Head, Emmy Noether Group, Institute of Human Genetics, University Hospital Bonn

The study group leader emphasizes the achievements of Hanna Zieger, who conducted the study as a lead author while doing her doctorate in medicine, much of it during the Coronavirus pandemic: “She has been learning the basics of data analytics at a tremendous speed and has programmed or adapted many of the analytics tools.”

At present, Hanna Zieger is finishing a part of her practical year in Dresden prior to graduating with her third state examination in medicine in the spring. Also, she plans to continue research after finishing her studies.

The research findings offer new perceptions of the biological mechanisms that might lead to cleft lip and palate. Subsequently, the study group plans to additionally assess the Gabriella Miller Kids First program data set and employ extra patient groups to explain in more detail whether and how other transcription factors also contribute to cleft lip and palate and how the risk variants communicate with one another.