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Non-syndromic cleft lip aetiology is illuminated by integrative approaches

In a recent study, researchers integrated existing genomic, epigenomic and transcriptomic data to generate novel insights into the aetiology of non-syndromic cleft lip with or without cleft palate.

Affecting ~1 in 1000 newborns, non-syndromic cleft lip with or without cleft palate (nsCL/P) is the most common facial disorder. It is a congenital birth defect stemming from failures in embryonic mid-facial development. Affected individuals are at heightened risk for adverse health outcomes later in life, such as middle ear fluid and hearing loss.

Genome-wide association studies (GWAS) have revealed at least 40 genetic loci significantly associated with increased risk of nsCL/P. However, there have been limited attempts to translate these statistical associations into functional mechanisms. As such, the molecular aetiology of nsCL/P is poorly understood.  

Novel risk loci for cleft lip

In this study, published in Human Genetics and Genomics, researchers revealed novel insights into nsCL/P aetiology. To do this, the team took advantage of existing nsCL/P GWAS and epigenetic data on mid-facial development. Headed by the Institute of Human Genetics, the group first combined GWAS data from across European, Asian and Latin America ethnicities.

This meta-analysis validated 40 known loci and revealed 5 novel loci underlying nsCL/P risk. The novel loci mapped to non-coding regions near genes involved in facial development, such as CAPZB, NBL1 and EYA2.

Genes, pathways and regulatory architecture of nsCL/P

To interpret genetic associations in the context of molecular processes underlying nsCL/P aetiology, the researchers further incorporated genome structure, gene expression and chromatin modification data into their analyses.

The team then illuminated the downstream effects of nSCL/P risk variants by identifying those located in topologically associated domains (TADs). These are regions of 3D genomic interactions involved in gene regulation. Within TADs located in GWAS loci, the researchers found 407 genes. Of these genes, 240 were previously shown by RNA-seq to be expressed in neural crest cells (NCCs). NCCs are multipotent cells that differentiate into various cell types, including craniofacial cells. Notably, biological pathways involved in regulatory processes and metabolism were exclusive to the NCC-expressed genes.

Taking the analysis further, the researchers illuminated the regulatory architecture of nsCL/P with existing epigenetic data. By using ChIP-seq, researchers have previously profiled chromatin modifications in the cell types and tissues involved in mid-facial development for the 4.5-10 week period after conception. In this study, researchers layered this data for NCCs and craniofacial tissue (CT) over GWAS loci. The results showed 23% of nsCL/P variants mapped to active chromatin states, while 14% mapped to bivalent or repressed chromatin states. In contrast, only 16% and 11% of the control variants mapped to active and bivalent or repressed states, respectively.

Integrative approaches reveal novel insights into disease

Limited data from other cell types has meant that not all the contributors to craniofacial development were included in this study. Nonetheless, new risk loci, pathways and regulatory architecture underlying nsCL/P development were revealed. This was enabled by the systematic merging of genomic, epigenomic and transcriptomic data.

GWAS has greatly increased our understanding of the genetic architecture of disease. However, the translation of statistical associations into functional mechanisms has lagged behind. As demonstrated by this study, integrating genetic data with other omics datasets may finally bridge this gap. Novel disease-associated loci and mechanisms can be revealed not just for nsCL/P but for other complex diseases.

Image credit: kjpargeter – Freepik

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Cleft lip / Multi-omics