Why HPV16? Why, now, HPV42? How the discovery of HPV42 in rare cancers provides an opportunity to challenge our understanding about the transition between health and disease for common members of the healthy microbiota

Abstract

In 2022, a bioinformatic, agnostic approach identified HPV42 as causative agent of a rare cancer, later confirmed experimentally. This unexpected association offers an opportunity to reconsider our understanding about papillomavirus infections and cancers. We have expanded our knowledge about the diversity of papillomaviruses and the diseases they cause. Yet, we still lack answers to fundamental questions, such as what makes HPV16 different from the closely related HPV31 or HPV33; or why the very divergent HPV13 and HPV32 cause focal epithelial hyperplasia, while HPV6 or HPV42 do not, despite their evolutionary relatedness. Certain members of the healthy skin microbiota are associated to rare clinical conditions. We propose that a focus on cellular phenotypes, most often transient and influenced by intrinsic and extrinsic factors, may help understand the continuum between health and disease. A conceptual switch is required towards an interpretation of biology as a diversity of states connected by transition probabilities, rather than quasi-deterministic programs. Under this perspective, papillomaviruses may only trigger malignant transformation when specific viral genotypes interact with precise cellular states. Drawing on Canguilhem's concepts of normal and pathological, we suggest that understanding the transition between fluid cellular states can illuminate how commensal-like infections transition from benign to malignant.

Keywords: cell type; diversity; ecology; evolution; genotype-to-phenotype; infection and cancer; microbiote; papillomavirus; phenotype; phenotype-to-environment; virome; virus–host interactions.

Figure 1.

Phylogeny, genomic, and phenotypic traits of Alpha- and DyoomikronPVs. Phylogenetic relationships inferred using maximum likelihood (RAxML) based on the concatenated e1e2l2l1 ORFs. Numbers in the branches present support after 5000 bootstrap cycles. The tree is rooted using DyoomikronPVs as outgroup. The four main clades within AlphaPVs are identified in blue, grey, green, and orange. Scalebar presents number of substitutions per site. species: taxonomy species for AlphaPVs. Genotypes labelled by an asterisk are not classified yet. host: taxonomy of the host for each genotype. e6_e7: organization of the e6e7 ORFs; red, e7 start precedes e6 stop with a range of 3–39 nucleotides; grey, means e7 start and e6 stop are merged in a TAATG sequence; and green, e6 stop precedes e7 start with a range of 2–17 nucleotides. Splicing: presence (green) or absence (red) of a splicing event in the e6 ORF either predicted (light colour) (Van Doorslaer et al. 2017) or experimentally confirmed (dark colour) (Cornelissen et al. , Nakagawa et al. , Sotlar et al. , Halec et al. 2013). p53: empirical evidence of E6 protein ability to induce degradation of p53 (Fu et al. , Mesplède et al. , Long et al. 2022). PBM: presence (green) or absence (red) of a C-terminal PDZ binding Motif (PBM) in the E6 protein. E5: type of E5 ORF found in each AlphaPV species (Bravo and Alonso 2004). Oncogenic potential: IARC/ICO classification for HPVs (HPV Information Centre ), and literature data for AlphaPVs-species-12 (Kloster et al. , Ostrow et al. , Chen et al. , , Bergin et al. , Long et al. 2022).

Figure 2.

Global scenario of AlphaPV evolution. Cartoon depicting the evolutionary relationships among the four large clades of AlphaPV species, with branches in blue, black, green, and orange. DyoomikronPVs are used as an outgroup. Branches comprising viruses not classified yet are labelled as t.b.n. (to be assigned). Blue and black boxes indicate the genomic organization of the e2l2 interface between early and late ORF cassettes, as well as the type of E5 protein encoded, if applicable. Red and orange boxes indicate the organization of the e6 and e7 ORFs, overlapping or not. The inset presents the evolutionary history of the host species, with the scale in millions of years before present. For each viral branch, coloured box matches the code for the corresponding host species. A time scale is included as a suggestion for the timing of the different evolutionary events in the history of AlphaPVs, assuming a large cophylogeny between viruses and hosts. The genome of the Alpha-DyoomikronPV ancestor, predating the split between Platyrrhini and Catarrhini, did not contain any region between early and late ORF casettes, and the e6 and e7 ORFs overlapped. In the genome of the AlphaPV ancestor, an integration event introduced a sequence between the early and the late gene cassettes. This individual event is possibly linked to the basal radiation in AlphaPVs that generated the extant four main clades, all of them spanning PVs infecting hosts in the Hominoidae and in the Cercopithecoidae primate families. Different types of E5 ORFs emerged separately in each of these large clades, and eventually disappeared in specific taxa, such as E5delta in HPV42, or were recently pseudogenized, such as E5_alpha in AlphaPVs species 5 and 6. In the genome of the ancestor of AlphaPVs species 5, 6, 7, 9, 11, and 12, an insertion occurred between the e6 and e7 ORFs, possibly linked to the emergence of the C-terminal PDZ binding Motif in the E6 protein, to the gain of function of E6 to induce degradation of p53 and to the appearance of the splicing event in the e6 ORF. This viral clade, labelled in orange, contains all (probably|possibly) oncogenic HPVs, classified after their oncogenic risk for anogenital and oropharyngeal cancers. HPV42 causative agent of DPA, a rare tumour of the sweat glands, is a member of AlphaPVs-species 1.

Figure 3.

Clustering of AlphaPVs after epidemiological characteristics and codon usage preferences. Principal component analyses for epidemiological variables (A) and for codon usage preferences (B) of AlphaHPVs. Values in the axes reflect the percentage of the total variance captured by the corresponding component. Viral species are stratified into the main four evolutionary clades. Numbers correspond to the HPV genotype. Epidemiological variables used: genotype-specific prevalence in asymptomatic cervical samples and in cervical, vaginal, vulvar, anal and penile cancers (HPV Information Centre ), genotype-specific median duration of the cervical infection (Goodman et al. , Trottier et al. , Schmeink et al. , Ramanakumar et al. 2016), and genotype-specific 1-year and 5-years cumulative first detections of cervical infection (Malagón et al. 2023). Codon usage was evaluated using the codon usage similarity index (COUSIN) for each of the e6, e7, e1, e2, l2, and l1 ORFs against the average human codon usage preferences (Bourret et al. 2019).