Supplementary data depicted in Supplementary Figures S1-S9

HPV42 is associated with DPA. A, Overview of unbiased screening approach for detection of vertebrate-infecting viruses in targeted next-generation sequencing (NGS) data. Targeted NGS data from 18 skin tumor types and MCC (positive control, pos. ctrl.) were analyzed with the centrifuge metagenomic classifier utilizing a custom viral database (Viral DB). B, Virus abundance score in targeted NGS data of 214 human tumor samples. Detection of HPV42 in 100% (n = 11/11) of DPA samples. ACC, adenoid cystic carcinoma; AFX, atypical fibroxanthoma; AS, angiosarcoma; BPDCN, blastic plasmacytoid dendritic cell neoplasm; DM, desmoplastic melanoma; DTE, desmoplastic trichoepithelioma; EPC, eccrine porocarcinoma; ES, eccrine spiradenoma; LM, lentigo maligna melanoma; MAC, microcystic adnexal carcinoma; PM, pediatric melanoma; PPT, proliferating pilar cystic tumor; SAC, spiradenocarcinoma; SC, sebaceous carcinoma; SGC, sweat gland carcinoma; SKCM, cutaneous melanoma. Viral prevalence: proportion of samples with detected virus in any given tumor type. Abundance score: mean proportion of detected virus in any given tumor type. C, HPV42 abundance score in a cohort of 17 DPAs after sequence capture to DNA and RNA of 6,453 viruses. White diamond: HPV42 detected but below an abundance of 1%. ND, not determined. D, Top, Circos plot depicting HPV42–human genome breakpoints. Each arch represents one detected breakpoint. Bottom, lollipop presentation of integration breakpoints in the HPV42 genome. Each lollipop represents one breakpoint (Supplementary Table S4). E, FISH signal of HPV42 genome (magenta) and human genome integration site adjacent locus (yellow) in DPA nuclei (blue). White arrowheads indicate fusion signals. Scale bar, 2.5 μm. Individual channels and quantifications in Supplementary Fig. S4. F, Top, RNA-ISH staining for expression of early region HPV42 mRNA in lung metastasis of a DPA tumor (T) and the surrounding normal (N) tissue. Scale bar, 1 mm. Bottom, inset. Scale bar, 20 μm.

Oncogenic HPVs induce a germ cell–like transcriptional program conserved throughout HPV-driven cancers. A, Overview of the random forest (RF) feature selection and machine learning procedure to identify a transcriptional fingerprint of HPV-driven oncogenesis. CESC and HNSCC expression data were annotated with HPV status (data acquisition), commonly differentially expressed genes between HPV+ and HPV− were identified (data preparation), and 12 protein-coding signature genes (RF12) were identified (feature selection). Four different machine learning models were trained with RF12 on a subset of DPA, CESC, and HNSCC samples (model training); the model with the best hyperparameters was evaluated using the withheld sample subset and used to classify Genotype-Tissue Expression (GTEx), skin warts, or normal skin expression data (deployment). B, Contribution of RF12 signature genes to cumulative feature importance (%) to discriminate between HPV+ and HPV− tumor samples. C, Uniform manifold approximation and projection (UMAP) dimensionality reduction of RF12 expression in DPA, CESC, HNSCC, and skin warts. D, HPV+ probability scores were calculated by RF12 for CESC, HNSCC, DPA, skin warts, and normal skin. For CESC, HNSCC, and DPA, the test set samples are displayed. E, HPV+ probability scores for HNSCC calculated for CDKN2A and SYCP2 alone, the combination of CDKN2A and SYCP2 (RF2), and RF12. F, HPV+ probability scores were calculated by RF12 for 31 normal tissues obtained from the GTEx database. G, Expression levels of RF12 genes in 15 cell types obtained from Human Protein Atlas. H, Schematic model of the germ cell–like program in HPV-driven cancer.

Viral abundance scores in ViroCap assay.

Transposable elements (TEs) are abundant in the human genome, and they provide the source for genetic and functional diversity. Previous studies have suggested that TEs are repressed by DNA methylation and chromatin modifications. Here through integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters (altPs) at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and the recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. Perturbation of hierarchical chromatin topology can lead to co-option of LTRs as functional altPs, driving aberrant transcriptional activation of oncogenes. These data uncovered a new layer of regulatory mechanisms of TE expression and posit TAD hierarchy dysregulation as a new mechanism for altP-mediated oncogene activation and transcriptional diversity in cancer.

The present case report describes a completely ulcerated infantile hemangioma (UIH) in a 5-month-old infant on the left proximolateral thigh initially misdiagnosed as pyoderma gangrenosum, sporotrichosis or atypical mycobacterial infection. Clinical assessment, histological findings, and GLUT‑1 immunohistochemistry confirmed the diagnosis of UIH. Systemic propranolol treatment led to rapid ulcer healing within 3 weeks and complete recovery without relapse after 18 months of treatment. The report emphasizes the diagnostic challenges, effective propranolol treatment and the importance of considering UIH in the differential diagnoses of solitary pediatric ulcers.

HPV42 induces transformation in vitro and tumor growth in vivo. A, Growth curves of HPKs transduced with the full genome of HPV11 (low-risk), HPV16 (high-risk), and HPV42. B, Crystal violet staining of MEF cells at day 14 after transduction. Scale bars, 100 μm. C, HPV42-E7 protein interaction partners identified in BioID proximity-labeling experiment. Pathway members of gene ontology terms G1–S transition (red) and HIPPO pathway (blue) are labeled. FC, fold change. D, E2F reporter assay in U2OS cells transduced with E7 proteins of HPV11, 16, or 42. ***, P < 0.001; ****, P < 0.0001 (one-way ANOVA, Tukey multiple comparisons test). E, Gene set enrichment analysis (GSEA) of the Molecular Signatures Database (MSigDB) hallmark gene set (top) and MSigDB curated gene set (bottom) comparing HPV42-E7 versus EV-transduced HPK cells. dev., development; NES, normalized enrichment score. F, IHC for YAP1 in a DPA tumor. Scale bar, main: 50 μm; inset: 3 mm. G, Individual tumor growth of EV- or E7 of HPV11-, HPV16-, or HPV42-transduced HaCaT cells in NSG mice. Each group consists of 5 mice (i.e., 10 tumors).

Transposable elements (TEs) are abundant in the human genome, and they provide the sources for genetic and functional diversity. The regulation of TEs expression and their functional consequences in physiological conditions and cancer development remain to be fully elucidated. Previous studies suggested TEs are repressed by DNA methylation and chromatin modifications. The effect of 3D chromatin topology on TE regulation remains elusive. Here, by integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. In cancer, perturbation of the hierarchical chromatin topology can lead to co-option of LTRs as functional alternative promoters in a context-dependent manner and drive aberrant transcriptional activation of novel oncogenes and other divergent transcripts. These data uncovered a new layer of regulatory mechanism of TE expression beyond DNA and chromatin modification in human genome. They also posit the TAD hierarchy dysregulation as a novel mechanism for alternative promoter-mediated oncogene activation and transcriptional diversity in cancer, which may be exploited therapeutically.

The tumour microenvironment is programmed by cancer cells and substantially influences anti-tumour immune responses1,2. Within the tumour microenvironment, CD8+ T cells undergo full effector differentiation and acquire cytotoxic anti-tumour functions in specialized niches3-7. Although interactions with type 1 conventional dendritic cells have been implicated in this process3-5,8-10, the underlying cellular players and molecular mechanisms remain incompletely understood. Here we show that inflammatory monocytes can adopt a pivotal role in intratumoral T cell stimulation. These cells express Cxcl9, Cxcl10 and Il15, but in contrast to type 1 conventional dendritic cells, which cross-present antigens, inflammatory monocytes obtain and present peptide-major histocompatibility complex class I complexes from tumour cells through 'cross-dressing'. Hyperactivation of MAPK signalling in cancer cells hampers this process by coordinately blunting the production of type I interferon (IFN-I) cytokines and inducing the secretion of prostaglandin E2 (PGE2), which impairs the inflammatory monocyte state and intratumoral T cell stimulation. Enhancing IFN-I cytokine production and blocking PGE2 secretion restores this process and re-sensitizes tumours to T cell-mediated immunity. Together, our work uncovers a central role of inflammatory monocytes in intratumoral T cell stimulation, elucidates how oncogenic signalling disrupts T cell responses through counter-regulation of PGE2 and IFN-I, and proposes rational combination therapies to enhance immunotherapies. Inflammatory monocytes are identified as important players in T cell restimulation in the tumour microenvironment.

PDF file - 65K, Supplemental Figure 1. Anatomical scheme of the eye.

Abstract The skin is exposed to viral pathogens, but whether they contribute to the oncogenesis of skin cancers has not been systematically explored. Here we investigated 19 skin tumor types by analyzing off-target reads from commonly available next-generation sequencing data for viral pathogens. We identified human papillomavirus 42 (HPV42) in 96% (n = 45/47) of digital papillary adenocarcinoma (DPA), an aggressive cancer occurring on the fingers and toes. We show that HPV42, so far considered a nononcogenic, “low-risk” HPV, recapitulates the molecular hallmarks of oncogenic, “high-risk” HPVs. Using machine learning, we find that HPV-driven transformation elicits a germ cell–like transcriptional program conserved throughout all HPV-driven cancers (DPA, cervical carcinoma, and head and neck cancer). We further show that this germ cell–like transcriptional program, even when reduced to the top two genes (CDKN2A and SYCP2), serves as a fingerprint of oncogenic HPVs with implications for early detection, diagnosis, and therapy of all HPV-driven cancers. Significance: We identify HPV42 as a uniform driver of DPA and add a new member to the short list of tumorigenic viruses in humans. We discover that all oncogenic HPVs evoke a germ cell–like transcriptional program with important implications for detecting, diagnosing, and treating all HPV-driven cancers. See related commentary by Starrett et al., p. 17. This article is highlighted in the In This Issue feature, p. 1

BACKGROUND:Despite the large number of articles published on skin lesions related to COVID-19, clinicopathological correlation has not been performed consistently and immunohistochemistry to demonstrate spike 3 protein expression has not been validated through RT-PCR.MATERIAL AND METHODS:We compiled 69 cases of patients with confirmed COVID-19, where skin lesions were clinically and histopathologically studied. Immunohistochemistry (IHC) and RT-PCR was performed in skin biopsies.RESULTS:After a careful review of the cases, 15 were found to be dermatosis not related to COVID-19, while the rest of the lesions could be classified according to their clinical characteristics as vesicular (4), maculopapular eruptions (41), urticariform (9), livedo and necrosis (10) and pernio-like (5). Although histopathological features were similar to previously reported results, we found two previously unreported findings, maculopapular eruptions with squamous eccrine syringometaplasia and neutrophilic epitheliotropism. IHC showed in some cases endothelial and epidermal staining but RT-PCR was negative in all the tested cases. Thus, direct viral involvement could not be demonstrated.CONCLUSIONS:Despite presenting the largest series of confirmed COVID-19 patients with histopathologically studied skin manifestations, direct viral involvement was difficult to establish. Vasculopathic and urticariform lesions seem to be those more clearly related to the viral infection, despite IHC or RT-PCR negative results failed to demonstrate viral presence. These findings, as in other dermatological areas, highlight the need of a clinico-pathological correlation to increase knowledge about viral involvement in COVID-19 skin-related lesions.

Despite the large number of articles published on skin lesions related to COVID-19, clinicopathological correlation has not been performed consistently and immunohistochemistry to demonstrate spike 3 protein expression has not been validated through RT-PCR.We compiled 69 cases of patients with confirmed COVID-19, where skin lesions were clinically and histopathologically studied. Immunohistochemistry (IHC) and RT-PCR was performed in skin biopsies.After a careful review of the cases, 15 were found to be dermatosis not related to COVID-19, while the rest of the lesions could be classified according to their clinical characteristics as vesicular (4), maculopapular eruptions (41), urticariform (9), livedo and necrosis (10) and pernio-like (5). Although histopathological features were similar to previously reported results, we found two previously unreported findings, maculopapular eruptions with squamous eccrine syringometaplasia and neutrophilic epitheliotropism. IHC showed in some cases endothelial and epidermal staining but RT-PCR was negative in all the tested cases. Thus, direct viral involvement could not be demonstrated.Despite presenting the largest series of confirmed COVID-19 patients with histopathologically studied skin manifestations, direct viral involvement was difficult to establish. Vasculopathic and urticariform lesions seem to be those more clearly related to the viral infection, despite IHC or RT-PCR negative results failed to demonstrate viral presence. These findings, as in other dermatological areas, highlight the need of a clinico-pathological correlation to increase knowledge about viral involvement in COVID-19 skin-related lesions.

How targeted therapies and immunotherapies shape tumors, and thereby influence subsequent therapeutic responses, is poorly understood. In the present study, we show, in melanoma patients and mouse models, that when tumors relapse after targeted therapy with MAPK pathway inhibitors, they are cross-resistant to immunotherapies, despite the different modes of action of these therapies. We find that cross-resistance is mediated by a cancer cell–instructed, immunosuppressive tumor microenvironment that lacks functional CD103+ dendritic cells, precluding an effective T cell response. Restoring the numbers and functionality of CD103+ dendritic cells can re-sensitize cross-resistant tumors to immunotherapy. Cross-resistance does not arise from selective pressure of an immune response during evolution of resistance, but from the MAPK pathway, which not only is reactivated, but also exhibits an increased transcriptional output that drives immune evasion. Our work provides mechanistic evidence for cross-resistance between two unrelated therapies, and a scientific rationale for treating patients with immunotherapy before they acquire resistance to targeted therapy. Obenauf and colleagues report that acquired resistance to BRAF and MEK inhibitors in melanoma confers cross-resistance to immune checkpoint blockade by fostering a cancer cell–instructed, immune-evasive tumor microenvironment.

Merkel cell carcinoma (MCC) is a highly aggressive, neuroendocrine skin cancer that lacks actionable mutations, which could be utilized for targeted therapies. Epigenetic regulators governing cell identity may represent unexplored therapeutic entry points. Here, we targeted epigenetic regulators in a pharmacological screen and discovered that the lysine‐specific histone demethylase 1A (LSD1/KDM1A) is required for MCC growth in vitro and in vivo. We show that LSD1 inhibition in MCC disrupts the LSD1‐CoREST complex leading to displacement and degradation of HMG20B (BRAF35), a poorly characterized complex member that is essential for MCC proliferation. Inhibition of LSD1 causes derepression of transcriptional master regulators of the neuronal lineage, activates a gene expression signature resembling normal Merkel cells, and induces cell cycle arrest and cell death. Our study unveils the importance of LSD1 for maintaining cellular plasticity and proliferation in MCC. There is also growing evidence that cancer cells exploit cellular plasticity and dedifferentiation programs to evade destruction by the immune system. The combination of LSD1 inhibitors with checkpoint inhibitors may thus represent a promising treatment strategy for MCC patients. This study identifies that the integrity of the LSD1‐CoREST complex is essential for Merkel cell carcinoma (MCC) proliferation and maintaining cell identity. LSD1 inhibition causes derepression of transcriptional regulators of the neuronal lineage and is a novel entry point for targeted therapies in MCC. This study identifies that the integrity of the LSD1‐CoREST complex is essential for Merkel cell carcinoma (MCC) proliferation and maintaining cell identity. LSD1 inhibition causes derepression of transcriptional regulators of the neuronal lineage and is a novel entry point for targeted therapies in MCC.

through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/BJD.19327 This article is protected by copyright. All rights reserved DR ISABEL COLMENERO (Orcid ID : 0000-0001-6859-187X) DR LUCERO NOGUERA-MOREL (Orcid ID : 0000-0001-5694-8536) DR ANGELA HERNANDEZ-MARTIN (Orcid ID : 0000-0001-7260-8718) DR THOMAS WIESNER (Orcid ID : 0000-0001-5877-2992) DR JOSE LUIS RODRIGUEZ-PERALTO (Orcid ID : 0000-0002-5400-0693) DR LUIS REQUENA (Orcid ID : 0000-0002-1045-4810) DR ANTONIO TORRELO (Orcid ID : 0000-0002-5940-6916)

We developed a functional lineage tracing tool termed CaTCH (CRISPRa tracing of clones in heterogeneous cell populations). CaTCH combines precise clonal tracing of millions of cells with the ability to retrospectively isolate founding clones alive before and during selection, allowing functional experiments. Using CaTCH, we captured rare clones representing as little as 0.001% of a population and investigated the emergence of resistance to targeted melanoma therapy in vivo.