Second-Hit, Postzygotic PMVK and MVD Mutations in Linear Porokeratosis

Abstract

Importance: Linear porokeratosis features linear and whorled configurations of keratotic papules and plaques, with coronoid lamellae present on histologic examination. Because linear porokeratosis manifests in the lines of Blaschko representing the dorsoventral migration patterns of keratinocyte precursors, it has been suggested that postzygotic somatic mutation underlies the disease. However, no genetic evidence has supported this hypothesis to date.

Objective: To identify genetic mutations associated with linear porokeratosis.

Design, setting, and participants: Paired whole-exome sequencing of affected skin and blood/saliva samples from 3 participants from 3 academic medical centers with clinical and histologic diagnoses of linear porokeratosis.

Interventions or exposures: Whole-exome sequencing of paired blood/saliva and affected tissue samples isolated from linear porokeratosis lesions.

Main outcomes and measures: Germline and somatic genomic characteristics of participants with linear porokeratosis.

Results: Of the 3 participants, 2 were male. Participant ages ranged from 5 to 20 years old. We found a combination of a novel germline mutation and a novel somatic mutation within affected tissue in all cases. One participant had a germline heterozygous PMVK c.329G>A mutation and a somatic copy-neutral loss of heterozygosity confined to the lesional skin, while a second had a germline heterozygous PMVK c.79G>T mutation and an additional PMVK c.379C>T mutation in the lesional skin. In a third participant, there was a germline splice-site mutation in MVD (c.70 + 5G>A) and a somatic deletion in MVD causing frameshift and premature codon termination within the lesional skin (c.811_815del, p.F271Afs*33 frameshift).

Conclusions and relevance: Our findings suggest that linear porokeratosis is associated with the presence of second-hit postzygotic mutations in the genes that encode enzymes within the mevalonate biosynthesis pathway, and provide further evidence that the mevalonate pathway may be a potential target for therapeutic intervention in porokeratosis.

Figure 1.. Clinical and Histologic Features of Linear Porokeratosis

A, Participant 1 presented with whorls of pink verrucous papules and plaques. B, Histopathologic examination of affected skin revealed striking columns of parakeratosis overlying hypogranulosis and dyskeratotic cells (corresponding to cornoid lamellae) alternating with hyperorthokeratosis, acanthosis, and papillomatosis. C, Participant 2 presented with extensive whorls of pink plaques, some covered with yellowish crusts, clinically thought to be inflammatory linear verrucous epidermal nevus. D, Histopathologic evaluation showed alternate parakeratosis overlying hypogranulosis (corresponding to wide cornoid lamellae) and orthokeratosis, acanthosis, and papillomatosis with perivascular and interstitial lymphocytic infiltrate in the superficial dermis. E, Participant 3 had linear erythematous depressed plaques with prominent keratotic collar at lesional borders. F, Histologic examination of affected skin showed subtle columns of parakeratosis overlying hypogranulosis alternating with orthokeratosis and mild acanthosis. Histologic slides stained with hematoxylin-eosin. Scale bar = 100 μm.

Figure 2.. Second-Hit Somatic Mosaicism for PMVK and MVD Mutations Associated With Linear Porokeratosis

Germline and somatic mutations were identified via whole-exome sequencing of DNA isolated from tissue and blood/saliva of all 3 participants. Sanger sequencing was used to confirm mutations found in exome sequencing data. A, In participant 1 there was a germline heterozygous PMVK p.R110Q mutation. This mutation was enriched in affected skin due to loss of heterozygosity. B, In participant 2 there was a germline heterozygous PMVK p.E27X mutation, as observed in blood and affected skin. C, In participant 2 there was also a somatic PMVK p.Q127X mutation in the affected skin leading to a compound heterozygous state. D, In participant 3 there was a germline heterozygous MVD c.70 + 5G>A mutation, as observed in the blood and affected skin. The same mutation was found in his mother (data not shown).

Figure 3.. Copy Neutral Loss of Heterozygosity Is Evident in Affected Tissue From Participant 1

Abbreviations: BAF, B-allele frequency; RQ, relative quantification; SVD, singular value decomposition; ZRPK, z-scores of reads per kilobase. A, B-allele frequency differences between the affected tissue and blood are plotted across the genome for participant 1 by chromosome and physical position. Dashed vertical lines separate individual chromosomes. Somatic loss of heterozygosity on chromosome 1q of participant 1 extends from 14.66 megabases to the telomere, and contains the PMVK gene. B, The CoNIFER program was used to detect copy number variations on chromosome 1. Singular value decomposition of standardized z-scores of reads per thousand bases, per million reads is plotted against positions on chromosome 1 and shows no evidence for copy number variation. C, This is further corroborated by comparative qPCR assessing the PMVK R110Q location. The fold change of the copy number of genomic PMVK from affected skin is calculated using relative quantification (RQ): RQ, 1.01 (range, 0.91-1.13) for affected skin when the blood of participant 1 was used as the reference sample.

Figure 4.. The Mevalonate Pathway

The mevalonate pathway is an essential metabolic pathway that uses acetyl–Coenzyme A (CoA) to produce sterols and isoprenoid metabolites that are essential for a broad range of metabolic processes. Genes previously found to be involved in familial porokeratosis are in bold. Dashed arrows indicate multiple processes. tRNA refers to transfer RNA. ^aGenes in which second-hit postzygotic mutations were identified.