Detection of HPV E7 Transcription at Single-Cell Resolution in Epidermis

Abstract

Persistent human papillomavirus (HPV) infection is responsible for at least 5% of human malignancies. Most HPV-associated cancers are initiated by the HPV16 genotype, as confirmed by detection of integrated HPV DNA in cells of oral and anogenital epithelial cancers. However, single-cell RNA-sequencing (scRNA-seq) may enable prediction of HPV involvement in carcinogenesis at other sites. We conducted scRNA-seq on keratinocytes from a mouse transgenic for the E7 gene of HPV16, and showed sensitive and specific detection of HPV16-E7 mRNA, predominantly in basal keratinocytes. We showed that increased E7 mRNA copy number per cell was associated with increased expression of E7 induced genes. This technique enhances detection of active viral transcription in solid tissue and may clarify possible linkage of HPV infection to development of squamous cell carcinoma.

Papillomavirus Immune Evasion Strategies Target the Infected Cell and the Local Immune System

“…To support the development of immunotherapy, access to better research tools are needed. Recently, the development of high-throughput single-cell RNA sequencing techniques have allowed researchers to characterize the heterogeneity and interconnection among tumor cells, stromal cells, and immune cells within the tumor environment (213, 214). The analysis of gene expression profiles at single-cell resolution may also help identify new immunotherapeutic targets.…”

Cytokine/chemokine profiles in squamous cell carcinoma correlate with precancerous and cancerous disease stage

“…6a) where AK prominently differ from surrounding skin through the up-regulation of proinflammatory cytokines, and two subsets of SCC can be differentiated from AK based on their proinflammatory cytokine/chemokine expression profile. Going forward, it is likely that single-cell transcriptomics and proteomics, and perhaps epigenomics applications in the study of skin cancer may shed light on the relatively unknown heterogenous processes that contribute to skin cancer development, including understanding how cutaneous SCC may arise 31 , as well as the complex immune interplay within the tumour microenvironment and how it influences the success of immunotherapies 32 .…”

SC1: A Tool for Interactive Web-Based Single Cell RNA-Seq Data Analysis

“…Lukowski et al (2018), a scRNA-Seq dataset describing the detection of HPV E7 transcription at single-cell resolution in the epidermis (referred to as HPV dataset),…”

“…To showcase the various SC1 workflow functionalities, we include examples from several publicly available datasets described in • Fletcher et al (2017), an olfactory stem cell scRN-Seq dataset (referred to as OSC dataset in the remainder of this manuscript), • Lukowski et al (2018), a scRNA-Seq dataset describing the detection of HPV E7 transcription at single-cell resolution in the epidermis (referred to as HPV dataset), We also describe several best practices when analyzing single cell data with SC1 using the datasets described in • Nevin et al (2020), this 10x Genomics dataset contains the scRNA-Seq data of FACSsorted CD3-CD19-single cells from SNS-ablated or control CT26 tumor-bearing BALB/c mice (SNS dataset), • Liao et al (2020), a 10x Genomics dataset that contains the T-cells subset extracted from the COVID-19 dataset of single cells from healthy controls and several several 5 . CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.…”