Mosaic Variant in ATP2C1 Presenting as Relapsing Linear Acantholytic Dermatosis: Case Report

Abstract

Relapsing Linear Acantholytic Dermatosis (RLAD) is a rare disease that manifests as recurring episodes of crusted and vesicular lesions distributed in a Blaschkoid pattern with histology resembling Hailey-Hailey or Darier’s disease. RLAD is hypothesized to be a mosaic form of a known acantholytic disorder, but this hypothesis has lacked genetic conformation. To determine the genetic abnormalities causing RLAD, we performed exome sequencing of affected tissue and blood in a single subject. Exome sequencing of an punch biopsy revealed a c.238A>T, p.(Lys80*) variant in ATP2C1 found in 26% of the reads from lesional skin but absent in germline DNA. This somatic variant causes a truncated protein that would likely result in loss of function. Our findings indicate that, in this patient, RLAD is a clinical presentation of type one segmental Hailey-Hailey disease.

Introduction:

Autosomal dominant skin diseases that typically present diffusely can also occasionally occur in segmental patterns. In type 1 segmental disease, a post zygotic variant occurs during embryogenesis resulting in both allelic heterozygosity and clinical disease restricted to a segment of skin that reflects the migration pattern of the of the original mutated cell and its progeny. Type 2 segmental diseases develops in heterozygous embryos that will later manifest diffuse disease. A loss of heterozygosity, that occurs during embryogenesis causes segmental homozygosity of the variant allele thereby resulting in more severe disease in a segmental pattern superimposed on the diffuse disease.

Relapsing Linear Acantholytic Dermatosis is a rare disease, first described in 1985¹. It is characterized by unilateral vesicular, bullous or crusted lesions that present in a Blaschkoid or zosteriform pattern. Histology of these lesions resembles Hailey-Hailey or Darier’s disease². In 1995, Duschet and coworkers speculated that RLAD may be a type 1 segmental disorder². However, to our knowledge, this hypothesis has never been experimentally verified. Poblete-Gutierrez and coworkers³ described a patient with known Hailey-Hailey disease that developed earlier and more severe lesions in a segmental pattern. The segmental lesions were superimposed on the typical diffuse disease. They further demonstrated that the segmental lesions were specifically caused by loss of heterozygosity of ATP2C1 resulting in homozygosity of the germline ATP2C1 variant. Although these authors demonstrated an elegant mechanism for type 2 mosaicism in segmental Hailey-Hailey disease, they did not address the causative gene in RLAD which is hypothesized to be an example of type 1 mosaicism. We tested the hypothesis that RLAD is a mosaic form of either Hailey-Hailey or Darier’s disease, which result from variants in ATP2C1 and ATP2A2 respectively^4,5,6.

Methods:

Samples:

Blood samples and an intact punch biopsy containing both dermis and epidermis were taken with informed consent under an approved protocol from the Carilion Clinic (Roanoke VA) institutional review board.

Sequencing:

Exome capture was performed using Agilent SureSelect Human All Exon UTR (v5) kit according to manufacturer’s protocol. Exome sequencing was performed with the Illumina Hiseq 125 cycle paired end sequencing v4 Protocol.

Bioinformatics:

Variants were identified and screened by the Sention TNseq Algorithm on the DNAnexus platform. Further visualization was performed on the Integrative Genomics Viewer (Broad Institute, Cambridge, MA).

Results:

A 47-year-old female presented with a several year history of an intermittent pruritic rash distributed in a Blaschkoid segment over the right chest wall. The eruption always recurred in the same area and was refractory to previous treatments that included high potency topical steroids, oral prednisone and tacrolimus ointment. The patient denied any family history of similar lesions. Physical exam revealed crusted papules and plaques in a segmental distribution on the right chest wall (Fig 1). A biopsy showed downward elongation of the rete with acantholysis, dyskeratosis and suprabasal clefting (Fig 2). The patient was diagnosed with RLAD and was started on dapsone, with minimal improvement. The patient was then started on oral retinoids but was lost to follow-up.

Fig 1A,B:

RLAD showing vesicles, crusted papules and plaques in a zosteriform distribution on the right chest wall. These photographs were taken one year apart.

Fig 2:

RLAD biopsy reveals downward elongation of the rete with acantholysis, dyskeratosis and suprabasal clefting. A: 4x, B: 20x

We screened the entire exome for coding variants present in greater than 10% of the reads in lesional skin but not significantly present in blood (greater than 1% of the reads). Only two variants passed our screen, c.238A>T in ATP2C1, and c.469G>A on the ZNRF2 gene. The c.238A>T in ATP2C1 was present in 26% of the reads. This ATP2C1 variant, p.(Lys80*), creates a premature stop codon in exon 4 (reference sequences: NM_001199179, NP_001186108). This variant was confirmed by Sanger sequencing of a PCR amplicon from the paraffin block that was originally used to diagnose the RLAD. We also Sanger sequenced exon 4 from an archived skin punch biopsy taken distant from the RLAD that showed a cutaneous tinea infection. The c.238A>T variant was not seen in this specimen of normal skin. We also found a second variant c.457C>T (p.(153Arg* ) predicted to cause a premature stop codon in exon 7 of ATP2C1. This c.457C>T variant was present in only 10/297 (3%) of the reads, could not be verified by Sanger sequencing, and is of uncertain significance. Finally, we performed a manual screen in the genome browser of exonic and intronic regions of ATP2A2, the gene whose identified variants may cause Darier’s disease, but failed to identify any somatic coding or non-coding variants.

Discussion:

Our findings support the hypothesis that post-zygotic variants in ATP2C1 causes RLAD. Variants in this gene cause Hailey-Hailey disease by decreasing levels of its protein product, secretory pathway Ca²⁺/Mn²⁺-ATPase pump type 1 (SPCA1)^7,8. Hailey-Hailey occurs in patients hemizygous for germline variants in ATP2C1^5,8. Known Hailey-Hailey variants occur throughout the gene without apparent hotspots⁸. However, the majority of Hailey-Hailey variants cause premature protein termination⁴ as do the mosaic variants in our patient. In the case presented, the premature stop codons, generated by the variants, occur early on in the mRNA and likely leads to loss of function of the resulting protein. Our genetic findings coupled with the observation that the skin histology in our patient resembles that of Hailey-Hailey disease⁶ suggests that the same underlying disease process is occurring in RLAD. We suspect that the variant identified in ZNRF2 is a silent mosaic change unrelated to the development of RLAD in this patient as there are currently no known ZNRF2 variants associated any form of acantholytic skin disease.

Under the mosaic model, a somatic variant acquired early on in development is passed on to daughter cells resulting in a cell lineage genetically distinct from the rest of the organism. The unilateral Blaschkoid pattern of RLAD reflects the migration of the mutated cell lineage. We identified a c.238A>T, p.(Lys80*) ATP2C1 variant in the affected segment likely to cause loss of protein function. The observed allele frequency below 50% was likely due to the presence of inflammatory and mesenchymal cells in the sample.

While we have successfully identified the underlying pathology of RLAD in this case, we cannot say if all cases of RLAD are due to variations in ATP2C1. However, our patient does validate the hypothesis that post zygotic variants in acantholytic disease genes can cause RLAD and suggests that systemic retinoids, which are effective for generalized Hailey-Hailey disease,⁹ may also be successful for RLAD. Future research is needed to identify the factors that cause periodic increases in disease activity that drive the relapsing nature of RLAD.

What is Already Known about this topic?

Relapsing Linear Acantholytic Dermatosis (RLAD) is postulated to be a mosaic form of Haley-Haley or Darrier’s disease, however this hypothesis has remained unproven and the putative gene and driving genetic variants have remained unknown.

What does this study add?

Exome sequencing, performed on lesional skin and matched blood, found RLAD lesions to be mosaic for variants causing a premature stop codon in the ATP2C1 gene. Our findings support the hypothesis that RLAD is a type 1 segmental form of Hailey-Hailey disease caused by post-zygotic variants in the ATP2C1 gene.