Tumorigenic activation around HPV integrated sites in head and neck squamous cell carcinoma

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated HPV DNA on host chromatin structure and gene regulation remains less understood. We investigated genome-wide patterns of HPV integrations and associated host gene expression changes in the context of host chromatin states and topologically associating domains (TADs). HPV integrations were significantly enriched in active chromatin regions and depleted in inactive ones. Interestingly, regardless of chromatin state, genomic regions flanking HPV integrations showed transcriptional upregulation. Nevertheless, upregulation (both local and long-range) was mostly confined to TADs with integration, but not affecting adjacent TADs. Few TADs showed recurrent integrations associated with overexpression of oncogenes within them (e.g. MYC, PVT1, TP63 and ERBB2) regardless of proximity. Hi-C and 4C-seq analyses in cervical cancer cell line (HeLa) demonstrated chromatin looping interactions between integrated HPV and MYC/PVT1 regions (~ 500 kb apart), leading to allele-specific overexpression. Based on these, we propose HPV integrations can trigger multimodal oncogenic activation to promote cancer progression.

Current and Emerging Diagnostic, Prognostic, and Predictive Biomarkers in Head and Neck Cancer

Head and neck cancers (HNC) are a biologically diverse set of cancers that are responsible for over 660,000 new diagnoses each year. Current therapies for HNC require a comprehensive, multimodal approach encompassing resection, radiation therapy, and systemic therapy. With an increased understanding of the mechanisms behind HNC, there has been growing interest in more accurate prognostic indicators of disease, effective post-treatment surveillance, and individualized treatments. This chapter will highlight the commonly used and studied biomarkers in head and neck squamous cell carcinoma.

Clinical application of CT-based radiomics model in differentiation between laryngeal squamous cell carcinoma and squamous cell hyperplasia

Objective

To evaluate the clinical application of the CT-based radiomics prediction model for discriminating SCC and SCH.

Methods

A total of 254 clinical samples were selected from 291 patients with larynx-occupying lesions who underwent primary surgery. All lesions were validated via histopathological examination at The Second Hospital of Jilin University between June 2004 and December 2019. All patients were randomly allocated to the training (n = 177) and validation (n = 77) cohorts. After the acquisition of CT images, manual 3D tumor segmentation was performed using the CT images of the arterial, venous, and non-contrast phases via ITK-SNAP software. Subsequently, radiomics features were extracted using A.K. software. Based on the above features, three different diagnostic models (CTN, CTA+CTV, and CTN+CTA+CTV) were constructed to classify squamous cell carcinoma (SCC) and squamous cell hyperplasia (SCH). Additionally, receiver operating characteristic (ROC) and decision curve analysis (DCA) curves were measured to evaluate the diagnostic characteristics and clinical safety of the proposed three prognostic models.

Results

In the radiomic prediction Model 1 (CTN), the area under the curve (AUC), accuracy, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the training cohorts in differentiating SCC and SCH were 0.883, 0.785, 0.645, 1.000, 1.000, and 0.648, while in the testing cohorts, these values were 0.852, 0.792, 0.66, 1.000, 1.000, and 0.652, respectively. In the radiomic prediction Model 2 (CTA+CTV), the AUC, accuracy, sensitivity, specificity, PPV, and NPV values of the training cohorts were 0.965, 0.91, 0.916, 0.9, 0.933, and 0.875, respectively, while in the testing cohorts, the corresponding values were 0.902, 0.805, 0.851, 0.733, 0.833, and 0.759, respectively. In the radiomic prediction Model 3(CTN+CTA+CTV), the AUC, accuracy, sensitivity, specificity, PPV, and NPV values of the training cohorts were 0.985, 0.944, 0.953, 0.929, 0.953, and 0.929, while in the testing cohorts, the corresponding values were 0.965, 0.857, 0.894, 0.8, 0.875, and 0.828, respectively.

Conclusion

The radiomic prediction Model 3, based on the arterial-venous-plain combined scan phase of CT, achieved promising diagnostic performance, expected to be regarded as a preoperative imaging tool in classifying SCC and SCH to guide clinicians to develop individualized treatment programs.

Genomic structures and regulation patterns at HPV integration sites in cervical cancer

Human papillomavirus (HPV) integration has been implicated in transforming HPV infection into cancer, but its genomic consequences have been difficult to study using short-read technologies. To resolve the dysregulation associated with HPV integration, we performed long-read sequencing on 63 cervical cancer genomes. We identified six categories of integration events based on HPV-human genomic structures. Of all HPV integrants, defined as two HPV-human breakpoints bridged by an HPV sequence, 24% contained variable copies of HPV between the breakpoints, a phenomenon we termed heterologous integration. Analysis of DNA methylation within and in proximity to the HPV genome at individual integration events revealed relationships between methylation status of the integrant and its orientation and structure. Dysregulation of the human epigenome and neighboring gene expression in cis with the HPV-integrated allele was observed over megabase-ranges of the genome. By elucidating the structural, epigenetic, and allele-specific impacts of HPV integration, we provide insight into the role of integrated HPV in cervical cancer.

HPV-positive murine oral squamous cell carcinoma: development and characterization of a new mouse tumor model for immunological studies

BACKGROUND

Infection with high-risk human papillomavirus (HPV) strains is one of the risk factors for the development of oral squamous cell carcinoma (OSCC). Some patients with HPV-positive OSCC have a better prognosis and respond better to various treatment modalities, including radiotherapy or immunotherapy. However, since HPV can only infect human cells, there are only a few immunocompetent mouse models available that enable immunological studies. Therefore, the aim of our study was to develop a transplantable immunocompetent mouse model of HPV-positive OSCC and characterize it in vitro and in vivo.

METHODS

Two monoclonal HPV-positive OSCC mouse cell lines were established by inducing the expression of HPV-16 oncogenes E6 and E7 in the MOC1 OSCC cell line using retroviral transduction. After confirming stable expression of HPV-16 E6 and E7 with quantitative real-time PCR and immunofluorescence staining, the cell lines were further characterized in vitro using proliferation assay, wound healing assay, clonogenic assay and RNA sequencing. In addition, tumor models were characterized in vivo in C57Bl/6NCrl mice in terms of their histological properties, tumor growth kinetics, and radiosensitivity. Furthermore, immunofluorescence staining of blood vessels, hypoxic areas, proliferating cells and immune cells was performed to characterize the tumor microenvironment of all three tumor models.

RESULTS

Characterization of the resulting MOC1-HPV cell lines and tumor models confirmed stable expression of HPV-16 oncogenes and differences in cell morphology, in vitro migration capacity, and tumor microenvironment characteristics. Although the cell lines did not differ in their intrinsic radiosensitivity, one of the HPV-positive tumor models, MOC1-HPV K1, showed a significantly longer growth delay after irradiation with a single dose of 15 Gy compared to parental MOC1 tumors. Consistent with this, MOC1-HPV K1 tumors had a lower percentage of hypoxic tumor area and a higher percentage of proliferating cells. Characteristics of the newly developed HPV-positive OSCC tumor models correlate with the transcriptomic profile of MOC1-HPV cell lines.

CONCLUSIONS

In conclusion, we developed and characterized a novel immunocompetent mouse model of HPV-positive OSCC that exhibits increased radiosensitivity and enables studies of immune-based treatment approaches in HPV-positive OSCC.