Investigating the Molecular Genetics and Viral Repertoire of Patients with Epidermodysplasia verruciformis
Epidermodysplasia verruciformis (EV) is a rare autosomal recessive skin disorder with a phenotype conditional on human papillomavirus (HPV). HPV infections are primarily universal and asymptomatic in the general population; however, in individuals with EV, they lead to the development of flat-like warts and red/brownish papules or pityriasis versicolor-like skin lesions, most often from childhood onwards. Most patients eventually develop non-melanoma skin cancer, mainly in areas of sun-exposed skin, later in life. Less than 500 cases with confirmed diagnoses have been characterized. At least half of the cases of typical EV (skin-limited manifestations) are caused by bi-allelic loss-of-function mutations in TMC6/EVER1 or TMC8/EVER2 or CIB1. EVER1, EVER2, and CIB1 form a complex, and the cellular and molecular basis of disease in CIB1-TMC/EVER-deficient patients is poorly understood. A defect of keratinocyte-intrinsic immunity to HPV (mostly β form) is suspected. Indeed, these patients are not susceptible to other infectious diseases and have apparently normal leukocyte development. In contrast, patients with an atypical form of EV due to inborn errors of T-cell immunity invariably develop clinical symptoms of EV in the context of other infectious diseases. The features of the typical and atypical forms of EV thus suggest that the control of β-HPV infections requires both EVER1/EVER2-dependent keratinocyte-intrinsic immunity and T cell-dependent adaptive immunity. This study aimed to analyze, in greater depth, the molecular and cellular basis of EV in an exceptionally large cohort of 50 patients with an initial diagnosis of EV. We performed a systematic, stepwise process of sequencing by total RNA sequencing (RNA-Seq). We modified existing bioinformatic pipelines for mutation detection from RNA-Seq and significantly increased the diagnostic rate. Homozygosity mapping was embedded into our pipelines to add another level of confidence in identifying pathogenic variants. The utilization of RNA-Seq as a first-tier diagnostic method in this study allowed us to profile the transcriptome for the consequences of variants of unknown significance (VUS) on the mRNA splicing process, providing information on altered gene expression and, in particular, profile the existing viruses with tropism to the skin such as HPVs. We developed a sequencing-based method called VirPy, an automated pipeline for concurrent detection of 926 viruses, including more than 400 HPVs, and corresponding human mutations. Identification of mutations will assist in genetic counseling, particularly in the case of multiplex consanguineous families with high recurrence risk, as illustrated by the extensive family pedigrees in our study. Knowledge of the mutations also provides basis for prenatal testing through invasive chorionic villus sampling, non-invasive fetal DNA analysis in the maternal circulation, or through preimplantation genetic testing. Additionally, these genetic results allow for the application of allele-specific therapies.
Saeidian, Amir Hossein, "Investigating the Molecular Genetics and Viral Repertoire of Patients with Epidermodysplasia verruciformis" (2022). ETD Collection for Thomas Jefferson University. AAI29067099.