Genome-wide single nucleotide polymorphism-based autozygosity mapping facilitates identification of mutations in consanguineous families with epidermolysis bullosa

Mutation update: The spectra of PLEC sequence variants and related plectinopathies

Plectin, encoded by PLEC, is a cytoskeletal linker of intermediate filaments expressed in many cell types. Plectin consists of three main domains that determine its functionality: the N-terminal domain, the Rod domain, and the C-terminal domain. Molecular defects of PLEC correlating with the functional aspects lead to a group of rare heritable disorders, plectinopathies. These multisystem disorders include an autosomal dominant form of epidermolysis bullosa simplex (EBS-Ogna), limb-girdle muscular dystrophy (LGMD), aplasia cutis congenita (ACC), and an autosomal recessive form of EBS, which may associate with muscular dystrophy (EBS-MD), pyloric atresia (EBS-PA), and/or congenital myasthenic syndrome (EBS-MyS). In this study, genotyping of over 600 Iranian patients with epidermolysis bullosa by next-generation sequencing identified 15 patients with disease-causing PLEC variants. This mutation update analyzes the clinical spectrum of PLEC in our cohort and in the literature and demonstrates the relationship between PLEC genotype and phenotypic manifestations. This study has integrated our seven novel PLEC variants and phenotypic findings with previously published data totaling 116 variants to provide the most complete overview of pathogenic PLEC variants and related disorders.

Recalcitrant Cutaneous Warts in a Family with Inherited ICOS Deficiency

Recalcitrant warts, caused by human papillomaviruses (HPVs), can be a cutaneous manifestation of inborn error of immunity. This study investigated the clinical manifestations, immunodeficiency, single-gene susceptibility, and HPV repertoire in a consanguineous family with severe sinopulmonary infections and recalcitrant warts. Clinical and immunologic evaluations, including FACS and lymphocyte transformation test, provided evidence for immunodeficiency. Combined whole-exome sequencing and genome-wide homozygosity mapping were utilized to disclose candidate sequence variants. Whole-transcriptome sequencing was used to concomitantly investigate the HPV genotypes and the consequences of detected sequence variants in the host. The proband, a male aged 41 years, was found to be homozygous for the c.6delG, p.Lys2Asnfs∗17 variant in ICOS, encoding the inducible T-cell costimulator. This variant was located inside the 5 megabase of runs of homozygosity on 2q33.2. RNA sequencing confirmed the deleteriousness of the ICOS variant in three skin biopsies revealing significant downregulation of ICOS and its ligand, ICOSLG. Reads unaligned to the human genome were applied to 926 different viruses, and α-HPV57, β-HPV107, β-HPV14, and β-HPV17 were detected. Collectively, we describe a previously unrecognized inborn error of T-cell immunity to HPVs, indicating that autosomal recessive ICOS deficiency can underlie recalcitrant warts, emphasizing the immunologic underpinnings of recalcitrant warts at the nexus of human and viral genomic variation.

Pathogenic DST sequence variants result in either epidermolysis bullosa simplex (EBS) or hereditary sensory and autonomic neuropathy type 6 (HSAN-VI)

DST encodes bullous pemphigoid antigen-1 (BPAG1), a protein with eight tissue-specific isoforms expressed in the skin, muscle, brain, and nerves. Accordingly, mutations in this gene are associated with epidermolysis bullosa simplex (EBS) and hereditary sensory and autonomic neuropathy type 6 (HSAN-VI). The genotypic spectrum is attested to by 19 distinct mutations but genotype-phenotype correlation for both disorders is not well established. In this study, we performed next-generation sequencing (NGS) on two families with different phenotypic presentations, one fetus (P1) with musculoskeletal and neurological malformations established by prenatal ultrasound and family history, and a 15-year-old female (P2) with skin blistering. P1 had a novel homozygous nonsense mutation, DST: NM_001144769, c.3805C>T, p.R1269* within a region of homozygosity (ROH). This mutation resides within the plakin domain of BPAG1 and ablates all isoforms of this protein, leading to novel extracutaneous phenotypes consistent with HSAN-VI in P1. P2 had a recurrent homozygous mutation DST: NM_001723.7, c.3370C>T, p.Gln1124* that presented with giant, trauma-induced skin blisters without extracutaneous involvement. This mutation is located within the coiled-coil domain present on the skin isoform of DST, BPGA1-e, associated with EBS. In summary, we report two families with pathogenic DST variants and expand the spectrum of DST genotype and phenotypes.

Homozygous MEFV Gene Variant and Pyrin-Associated Autoinflammation With Neutrophilic Dermatosis: A Family With a Novel Autosomal Recessive Mode of Inheritance

Importance

Pyrin-associated autoinflammation with neutrophilic dermatosis (PAAND) is a monogenic autoinflammatory disorder with autosomal dominant inheritance and has been associated with monoallelic p.Ser242Arg and p.Glu244Lys variations in the MEFV gene. This dermatosis shares clinical features and pathogenesis with familial Mediterranean fever, although it is a clinically distinct entity.

Objective

To identify the genetic basis of PAAND in a consanguineous family with 2 affected children and to prescribe an effective genotype-guided treatment.

Design, Setting, and Participants

This case series study examined 2 siblings who presented with clinical features of PAAND. We sought the genetic basis of this disease with trio whole exome sequencing (trio-WES). Genome-wide homozygosity mapping provided additional evidence for causality of a sequence variant identified by trio-WES.

Main Outcomes and Measures

Association of a biallelic MEFV variation with a new form of autosomal recessive PAAND was documented by genetic analysis. Response to treatment with colchicine and a low-dose steroid was assessed clinically and experimentally.

Results

Two siblings, a girl (proband; age 5 years) and a boy (age 2.5 years) of Iranian-Azeri ancestry born to first-cousin consanguineous parents presented with clinical features of PAAND-recurrent episodes of maculopapular and pustular rash, gastrointestinal involvement resembling inflammatory bowel disease, and intussusception with generalized mesenteric lymphadenitis. A trio-WES test detected a previously unreported homozygous missense variation, p.Ser242Gly, in both patients' MEFV gene. Genome-wide homozygosity mapping revealed shared regions of homozygosity in the patients' DNA, including 1 on chromosome 16 harboring MEFV. Whole transcriptome sequencing by RNA-sequencing revealed that the variant MEFV transcript, among the inflammasome-associated transcripts, was most upregulated, and the cell-cell receptor interaction and innate immune system pathways were most positively enriched. Under the guidance of MEFV genotype, treatment with colchicine (1 mg/d) and low-dose prednisolone (2.5 mg every other day) was started, and the patients responded well.

Conclusions and Relevance

This case series study demonstrated successful genotype-guided treatment with colchicine and low-dose prednisolone, a low-cost therapeutic option with minimal adverse effects, in patients with a novel form of autosomal recessive PAAND. This case report examines the genetic basis of PAAND in a consanguineous family with 2 affected children and seeks to prescribe an effective genotype-guided treatment.

Kindler epidermolysis bullosa-like skin phenotype and downregulated basement membrane zone gene expression in poikiloderma with neutropenia and a homozygous USB1 mutation

Epidermolysis bullosa (EB) is a genotypically heterogeneous group of disorders characterized by cutaneous blistering and erosions with a tremendous spectrum of severity. One of the distinct forms of EB, Kindler EB (KEB), manifests with blistering and poikiloderma; this subtype of EB is caused by mutations in the FERMT1 gene encoding kindlin-1. In this study, we investigated a patient clinically diagnosed as KEB with reduced FERMT1 gene expression and intensity of immunostaining for kindlin-1. Transmission electron microscopy showed lamina densa reduplication, frequently observed in KEB. However, no mutations were identified in FERMT1 in this patient with consanguineous parents, and this gene resided outside of genomic regions of homozygosity (ROH). Instead, whole-exome sequencing and homozygosity mapping identified a homozygous sequence variant at the +4 position of intron 2 in the USB1 gene, encoding an exoribonuclease required for processing of U6 snRNA, a critical component of spliceosomes. Examination of the patient's RNA by RNA-Seq confirmed the pathogenicity of this variant, causing aberrant splicing predicted to result in loss of function of USB1. Mutations in this gene have been reported in patients with poikiloderma and neutropenia, with a few reported cases in association with skin fragility, a condition distinct from the KEB phenotype. Transcriptome analysis revealed that several genes, expressed in the cutaneous basement membrane zone and previously associated with different subtypes of EB, were differentially downregulated at the mRNA level. EB-associated mRNA downregulation was confirmed at protein levels by skin immunofluorescence. These observations provide a novel mechanism for blistering and erosions in the skin as a result reduced presence of adhesion complexes critical for stable association of epidermis and dermis at the level of cutaneous basement membrane zone.

Whole-Transcriptome Analysis by RNA Sequencing for Genetic Diagnosis of Mendelian Skin Disorders in the Context of Consanguinity

BACKGROUND

Among the approximately 8000 Mendelian disorders, >1000 have cutaneous manifestations. In many of these conditions, the underlying mutated genes have been identified by DNA-based techniques which, however, can overlook certain types of mutations, such as exonic-synonymous and deep-intronic sequence variants. Whole-transcriptome sequencing by RNA sequencing (RNA-seq) can identify such mutations and provide information about their consequences.

METHODS

We analyzed the whole transcriptome of 40 families with different types of Mendelian skin disorders with extensive genetic heterogeneity. The RNA-seq data were examined for variant detection and prioritization, pathogenicity confirmation, RNA expression profiling, and genome-wide homozygosity mapping in the case of consanguineous families. Among the families examined, RNA-seq was able to provide information complementary to DNA-based analyses for exonic and intronic sequence variants with aberrant splicing. In addition, we tested the possibility of using RNA-seq as the first-tier strategy for unbiased genome-wide mutation screening without information from DNA analysis.

RESULTS

We found pathogenic mutations in 35 families (88%) with RNA-seq in combination with other next-generation sequencing methods, and we successfully prioritized variants and found the culprit genes. In addition, as a novel concept, we propose a pipeline that increases the yield of variant calling from RNA-seq by concurrent use of genome and transcriptome references in parallel.

CONCLUSIONS

Our results suggest that "clinical RNA-seq" could serve as a primary approach for mutation detection in inherited diseases, particularly in consanguineous families, provided that tissues and cells expressing the relevant genes are available for analysis.

Research Techniques Made Simple: Whole-Transcriptome Sequencing by RNA-Seq for Diagnosis of Monogenic Disorders

Mendelian disorders with cutaneous manifestations comprise a genotypically heterogeneous group of over 1,000 diseases, and in most of them mutant genes have been identified. Mutation detection approaches in these diseases have largely focused on DNA analysis by next-generation sequencing techniques, including gene-targeted sequencing panels as well as whole-exome and whole-genome sequencing. Genome-wide homozygosity mapping (HM), based on DNA polymorphism, has also assisted in the identification of candidate genes in families with consanguinity. However, specific pathogenic variants have not been disclosed in many individual patients when analyzed by next-generation sequencing, and in particular, DNA-based analysis failed to identify many of the mutations impacting on splicing or gene expression. Whole-transcriptome sequencing by RNA sequencing (RNA-Seq), with appropriate bioinformatics, provides a robust tool to identify additional mutations to facilitate genetic diagnosis in genodermatoses. RNA-Seq can be used for variant calling and HM similar to DNA-based approaches, but it also allows for the identification of mutations that result in aberrant transcriptome expression, as displayed by heatmap analysis, and altered splicing patterns of RNA, as visualized by Sashimi plots. Thus, clinical RNA-Seq extends molecular diagnostics of rare genodermatoses, and it could provide a reliable first-tier diagnostic approach to extend mutation databases in patients with heritable skin diseases.

Arrhythmogenic right ventricular cardiomyopathy in patients with biallelic JUP-associated skin fragility

Arrhythmogenic right ventricular cardiomyopathy (ARVC), with skin manifestations, has been associated with mutations in JUP encoding plakoglobin. Genotype–phenotype correlations regarding the penetrance of cardiac involvement, and age of onset have not been well established. We examined a cohort of 362 families with skin fragility to screen for genetic mutations with next-generation sequencing-based methods. In two unrelated families, a previously unreported biallelic mutation, JUP: c.201delC; p.Ser68Alafs^*92, was disclosed. The consequences of this mutation were determined by expression profiling both at tissue and ultrastructural levels, and the patients were evaluated by cardiac and cutaneous work-up. Whole-transcriptome sequencing by RNA-Seq revealed JUP as the most down-regulated gene among 21 skin fragility-associated genes. Immunofluorescence showed the lack of plakoglobin in the epidermis. Two probands, 2.5 and 22-year-old, with the same homozygous mutation, allowed us to study the cross-sectional progression of cardiac involvements in relation to age. The older patient had anterior T wave inversions, prolonged terminal activation duration (TAD), and RV enlargement by echocardiogram, and together with JUP mutation met definite ARVC diagnosis. The younger patient had no evidence of cardiac disease, but met possible ARVC diagnosis with one major criterion (the JUP mutation). In conclusion, we identified the same biallelic homozygous JUP mutation in two unrelated families with skin fragility, but cardiac findings highlighted age-dependent penetrance of ARVC. Thus, young, phenotypically normal patients with biallelic JUP mutations should be monitored for development of ARVC.

Mycophenolate mofetil treatment of an H syndrome patient with a SLC29A3 mutation

H syndrome is a complex multi-organ disorder with autosomal recessive inheritance. The skin manifestations include early onset hyperpigmentation and hypertrichosis, followed by skin induration often diagnosed as scleromyxedema and morphea. There is no effective treatment. Our objective was to study the efficacy of mycophenolate mofetil in a patient with genetically confirmed H syndrome. We sought the genetic cause of H syndrome with whole-exome sequencing (WES) of the proband. Genome-wide homozygosity mapping (HM) provided additional evidence for causality of the variant suggested by WES. Here, we report a patient with characteristic clinical features of H syndrome, and the diagnosis was confirmed by identification of a homozygous SLC29A3 mutation (p.Gly437Arg). The patient was initially treated with prednisolone and cyclosporine, but after development of side-effects she was placed on mycophenolate mofetil. After the treatment with mycophenolate mofetil was initiated, resolution of hyperpigmentation was noted, and no new lesions developed during an 18-month follow-up period. Thus, mycophenolate mofetil could be considered as a safe and partially effective treatment of H syndrome.

Genomics-based treatment in a patient with two overlapping heritable skin disorders: Epidermolysis bullosa and acrodermatitis enteropathica

Next-generation sequencing (NGS) is helpful in diagnosing complex genetic disorders and phenotypes, particularly when more than one overlapping condition is present. From a large cohort of 362 families with clinical manifestations of skin and mucosal fragility, referred by several major medical centers, one patient was found by NGS to have two overlapping heritable skin diseases, recessive dystrophic epidermolysis bullosa (RDEB; COL7A1 mutations) and acrodermatitis enteropathica (AE; SLC39A4 mutations). The pathogenicity of the variants was studied at gene expression as well as ultrastructural and tissue levels. Although there is no specific treatment for RDEB except avoiding trauma, supplementation with oral zinc (3 mg·kg^-1 ·day^-1 ) for the AE resulted in rapid amelioration of the skin findings. This case demonstrates the power of NGS in identifying two genetically unlinked diseases that led to effective treatment with major clinical benefits as an example of genomics-guided treatment.

Hypotrichosis with juvenile macular dystrophy: Combination of whole-genome sequencing and genome-wide homozygosity mapping identifies a large deletion in CDH3 initially undetected by whole-exome sequencing-A lesson from next-generation sequencing

BACKGROUND

Hypotrichosis with juvenile macular dystrophy (HJMD) is an autosomal recessive disorder characterized by abnormal growth of scalp hair and juvenile macular degeneration leading to blindness. We have explored the genetic basis of HJMD in a large consanguineous family with 12 affected patients, 1-76 years of age, with characteristic phenotypes.

METHODS

We first applied genome-wide homozygosity mapping to 10 affected individuals for linkage analysis to identify the genomic region of the defective gene. All affected individuals shared a 7.2 Mb region of homozygosity on chromosome 16q21-22.3, which harbored 298 genes, including CDH3, previously associated with HJMD. However, whole-exome sequencing (WES) failed to identify the causative mutation in CDH3.

RESULTS

Further investigation revealed a missense variant in a gene closely linked to CDH3 (1.4 Mb distance: FHOD1: c.1306A>G, p.Arg436Gly). This variant was homozygous in all affected individuals and heterozygous in 18 out of 19 obligate carriers. While this variant was found by bioinformatics predictions to be likely pathogenic, a knock-in mouse for this variant, made by the CRISPR/Cas, showed no disease phenotype. However, using whole-genome sequencing (WGS), we were able to identify a novel Alu recombination-mediated deletion in CDH3:c.del161-811_246 + 1,044.

CONCLUSION

WGS was able to identify a deep intronic deletion mutation, not detected by WES.

Clinical practice guidelines for laboratory diagnosis of epidermolysis bullosa

Linked Comment: https://doi.org/10.1111/bjd.18377.

https://doi.org/10.1111/bjd.18829 available online

Molecular genetics of a cohort of 635 cases of phenylketonuria in a consanguineous population

Phenylketonuria (PKU) is an inborn error of amino acid metabolism caused by mutations in the phenylalanine hydroxylase (PAH) gene, characterized by intellectual deficit and neuropsychiatric complications in untreated patients with estimated frequency of about one in 10,000 to 15,000 live births. PAH deficiency can be detected by neonatal screening in nearly all cases with hyperphenylalaninemia on a heel prick blood spot. Molecular testing of the PAH gene can then be performed in affected family members. Herein, we report molecular study of 635 patients genetically diagnosed with PKU from all ethnicities in Iran. The disease-causing mutations were found in 611 (96.22%) of cases. To the best of our knowledge, this is the most comprehensive molecular genetics study of PKU in Iran, identifying 100 distinct mutations in the PAH gene, including 15 previously unreported mutations. Interestingly, we found unique cases of PKU with uniparental disomy, germline mosaicism, and coinheritance with another Mendelian single-gene disorder that provides new insights for improving the genetic counseling, prenatal diagnosis (PND), and/or pre-implantation genetic diagnosis (PGD) for the inborn error of metabolism group of disorders.

Recent advances in understanding and managing epidermolysis bullosa

Epidermolysis bullosa (EB) is a clinically and genetically heterogeneous skin fragility disorder characterized by trauma-induced skin dissociation and the development of painful wounds. So far, mutations in 20 genes have been described as being associated with more than 30 clinical EB subtypes. The era of whole-exome sequencing has revolutionized EB diagnostics with gene panels being developed in several EB centers and allowing quicker diagnosis and prognostication. With the advances of gene editing, more focus has been placed on gene editing-based therapies for targeted treatment. However, their implementation in daily care will still take time. Thus, a significant focus is currently being placed on achieving a better understanding of the pathogenetic mechanisms of each subtype and using this knowledge for the design of symptom-relief therapies, i.e. treatment options aimed at ameliorating and not curing the disease.