Whole transcriptome–based skin virome profiling in typical epidermodysplasia verruciformis reveals α-, β-, and γ-HPV infections
Amir Hossein Saeidian, Leila Youssefian, Mahtab Naji, Hamidreza Mahmoudi, Samantha M. Barnada, Charles Huang, Karim Naghipoor, Amir Hozhabrpour, Jason S. Park, Flavia Manzo Margiotta, Fatemeh Vahidnezhad, Zahra Saffarian, Kambiz Kamyab-Hesari, Mohammad Tolouei, Niloofar Faraji, Seyyede Zeinab Azimi, Ghazal Namdari, Parvin Mansouri, Jean-Laurent Casanova, Vivien Béziat, Emmanuelle Jouanguy, Jouni Uitto, Hassan Vahidnezhad
Amir Hossein Saeidian, Leila Youssefian, Mahtab Naji, Hamidreza Mahmoudi, Samantha M. Barnada, Charles Huang, Karim Naghipoor, Amir Hozhabrpour, Jason S. Park, Flavia Manzo Margiotta, Fatemeh Vahidnezhad, Zahra Saffarian, Kambiz Kamyab-Hesari, Mohammad Tolouei, Niloofar Faraji, Seyyede Zeinab Azimi, Ghazal Namdari, Parvin Mansouri, Jean-Laurent Casanova, Vivien Béziat, Emmanuelle Jouanguy, Jouni Uitto, Hassan Vahidnezhad
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Research Article Dermatology Genetics

Whole transcriptome–based skin virome profiling in typical epidermodysplasia verruciformis reveals α-, β-, and γ-HPV infections

Abstract

HPVs are DNA viruses include approximately 450 types that are classified into 5 genera (α-, β-, γ-, μ-, and ν-HPV). The γ- and β-HPVs are present in low copy numbers in healthy individuals; however, in patients with an inborn error of immunity, certain species of β-HPVs can cause epidermodysplasia verruciformis (EV), manifesting as recalcitrant cutaneous warts and skin cancer. EV presents as either typical or atypical. Manifestations of typical EV are limited to the skin and are caused by abnormal keratinocyte-intrinsic immunity to β-HPVs due to pathogenic sequence variants in TMC6, TMC8, or CIB1. We applied a transcriptome-based computational pipeline, VirPy, to RNA extracted from normal-appearing skin and wart samples of patients with typical EV to explore the viral and human genetic determinants. In 26 patients, 9 distinct biallelic mutations were detected in TMC6, TMC8, and CIB1, 7 of which are previously unreported to our knowledge. Additionally, 20 different HPV species, including 3 α-HPVs, 16 β-HPVs, and 1 γ-HPV, were detected, 8 of which are reported here for the first time to our knowledge in patients with EV (β-HPV-37, -47, -80, -151, and -159; α-HPV-2 and -57; and γ-HPV-128). This study expands the TMC6, TMC8, and CIB1 sequence variant spectrum and implicates new HPV subtypes in the pathogenesis of typical EV.

Authors

Amir Hossein Saeidian, Leila Youssefian, Mahtab Naji, Hamidreza Mahmoudi, Samantha M. Barnada, Charles Huang, Karim Naghipoor, Amir Hozhabrpour, Jason S. Park, Flavia Manzo Margiotta, Fatemeh Vahidnezhad, Zahra Saffarian, Kambiz Kamyab-Hesari, Mohammad Tolouei, Niloofar Faraji, Seyyede Zeinab Azimi, Ghazal Namdari, Parvin Mansouri, Jean-Laurent Casanova, Vivien Béziat, Emmanuelle Jouanguy, Jouni Uitto, Hassan Vahidnezhad

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Figure 11

A homozygous nonsense CIB1 founder mutation shared across 2 unrelated families with typical EV.

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A homozygous nonsense CIB1 founder mutation shared across 2 unrelated fa...
(A and G) Family pedigrees and clinical features of patients with CIB1 mutation. Note the parental consanguinity and multiple hematological and cutaneous malignancies within the extended families. (B and H) Multiple confluent pityriasis versicolor–like warts and BCC in the probands were observed, as shown in Figure 1C. Histopathology of the lesions showed orthokeratosis, hypergranulosis, and papillomatosis with dyskeratotic cells, and some keratinocytes of the upper squamous layer had vacuoles in their cytoplasm with nuclear inclusion, consistent with the diagnosis of HPV infection. Excisional biopsy from scalp lesion showed atypical squamoproliferative tumor with invasive buds (upper right panel). (C and I) Stepwise bioinformatic filtering on the data generated from RNA-Seq reduced the number of candidate variants leading to the identification of CIB1 as the candidate gene. (D and J) The mutation, CIB1: NM_006384.3, Exon 3, c.124C>T, p.Gln42*, was confirmed as homozygous in the probands through Sanger sequencing. (E) Heatmap expression profiling of RNA-Seq data displays significantly reduced CIB1 mRNA levels in the proband of family 9, compared with randomly selected housekeeping genes and other EV-associated genes, suggesting nonsense-mediated mRNA decay. (F and L) Sashimi plot (patient 17) showing the identification and quantification of full-length β-HPV-14, via VirPy, with expression in the wart and no expression in normal-appearing skin biopsy specimens of the proband. β-HPV-14, -22, and -21 were detected in the wart of patient 18. (K) To determine whether the mutation detected in these 2 families is a hot-spot mutation or a founder-effect mutation, we compared rare homozygous SNVs surrounding the CIB1 locus in chromosome 15, region q26.1, called from RNA-Seq data. Note conservation of the polymorphic markers within an 8.3 Mb block of DNA flanking the CIB1 locus. Created with BioRender.com. 1000G, 1000 Genomes Project; Exome Aggregation Consortium; URR, upstream regulatory region.