A recent study published in Nature Communications identifies rare genetic variants in families with rosacea.
Study: Whole genome sequencing identifies genetic variants associated with neurogenic inflammation in rosacea. Image Credit: STEKO / Shutterstock.com
What is rosacea?
Rosacea is a chronic skin disorder that is characterized by erythema, flushing, telangiectasia, hyperplasia, pustules/papules, or a combination of these symptoms. Rosacea prevalence has been estimated at 3.48% in the Chinese population.
Although the pathogenesis of rosacea remains unclear, endogenous and environmental factors have been reported to stimulate the augmentation of abnormal immune responses and neurovascular dysregulation.
Genetics may represent an endogenous factor contributing to rosacea development, as North European and Celtic descendants, as well as individuals with fair skin, are more affected by this skin condition, whereas Asians and African Americans are less affected. Several rosacea-associated genetic variants have been identified in genome-wide association studies.
Previous studies indicate a positive association between family history and rosacea risk, thus suggesting familial inheritance. Recent advances in high-throughput sequencing, whole-genome (WGS), and whole-exome (WES) sequencing, particularly family-based WES or WGS analyses, offer an excellent platform to explore rare genetic variants and their role in the development of rosacea.
About the study
In the present study, researchers perform WES and WGS analyses of samples from rosacea families to explore rare genetic variants. To this end, three large families with rosacea were identified for WGS analysis as the discovery cohort from the Han population in Hunan, China. Additionally, 49 small families with rosacea from Hunan and adjacent provinces served as the validation cohort.
From these samples, genomic DNA was extracted and used for WGS and WES analyses for both the discovery and validation cohort samples, respectively. Reads were abandoned if adaptor sequences were present or uncertain bases and low-quality bases constituted more than 10% and 50%, respectively. Reads were mapped to a reference human genome.
Variants with minor allele frequencies of less than 1% were defined as rare. Rare single deleterious variants were identified in leucine-rich repeat containing 4 (LRRC4), SH3, and PX Domains 2A (SH3PXD2A), as well as solute carrier family 26 member 8 (SLC26A8) genes in families one, two, and three, respectively.
Study findings
Amino acids corresponding to these sites were highly conserved across species. Several rare variants were also identified in validation cohort samples. Additional variants that were not identified in the discovery cohort were detected in SH3PXD2A and SLC26A8 genes in samples from two families in the validation cohort.
LRRC4 variants were not detected in validation cohort samples. Regardless, splice sites and missense variants were detected in numerous LRR family genes. Variant genes were ranked by their biological function in neurological processes to identify potential variants involved in neurogenic inflammation.
Overall, 28 genes with rare variants were identified in 33 families, several of which were in protocadherin alpha 5 (PCDHA5) in three independent families. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and gene ontology (GO) analyses revealed the clustering of variant genes within the neural synaptic function, depression, and peptidyl-tyrosine dephosphorylation, thus implying a link to neural function.
These observations led researchers to evaluate how variant gene mutations would impact rosacea development. To this end, single-cell RNA sequencing (scRNA-seq) was performed, which showed high expression levels of LRRC4, SH3PXD2A, and SLC26A8 genes in neural cells. Subsequently, the researchers overexpressed mutants of these genes with corresponding gene variants in neural cells and analyzed the expression of different neuropeptides. Significantly higher expression of multiple vasoactive neuropeptides was observed in mutant neural cells.
A mouse model with an L385P mutation, which is the human equivalent of L386P, in the Lrrc4 gene was also generated. Cathelicidin LL37 was administered twice daily for two days to wild-type and mutant mice to create rosacea-like mouse models.
Twelve hours after LL37 treatment, wild-type mice exhibited prominent rosacea-like characteristics, whereas the mutant mice displayed significantly worse features. RNA was then extracted from dorsal root ganglions (DRGs) in wild-type and mutant mice, which led to the identification of 37 differentially expressed genes.
The vasoactive intestinal peptide (Vip) gene was the most upregulated gene. Immunostaining confirmed that VIP expression significantly increased in mutant DRGs after LL37 administration as compared to wild-type mice. Moreover, blocking VIP signaling with an antagonist peptide of the VIP receptor led to improvements in rosacea-like dermatitis in mutant mice.
Conclusions
The researchers identified LRRC4, SLC26A8, and SH3PXD2A, each of which had a distinct rare genetic variant, as potential genes responsible for rosacea susceptibility. Pathway analyses highlighted the functional role of these genes in synaptic function, neural cell adhesion, neuroactive ligand-receptor interaction, and depression, which is consistent with prior findings that the gene set involved in chemical synapse transmission was upregulated in rosacea lesions.
Taken together, the study findings revealed the genetic basis and heterogeneity of familial inheritance and neurogenic inflammation of rosacea.
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