Human papillomavirus integration transforms chromatin to drive oncogenesis.

Background: Human papillomavirus (HPV) drives almost all cervical cancers and up to 70% of head and neck cancers. Frequent integration into the host genome occurs predominantly in tumorigenic types of HPV. We hypothesize that changes in chromatin state at the location of integration can result in changes in gene expression that contribute to the tumorigenicity of HPV.

Cell-free DNA topology depends on its subcellular and cellular origins in cancer.

Cancer cells release large quantities of cell-free DNA (cfDNA) into the surrounding tissue and circulation. As cfDNA is a common source of biomarkers for liquid biopsy and has been implicated as a functional mediator for intercellular communication, fundamental characterization of cfDNA topology has widespread biological and clinical ramifications. Whether the topology of cfDNA is such that it exists predominantly in membrane-bound extracellular vesicles (EVs) or in nonvesicular DNA-protein complexes remains poorly understood.

HPV Sequencing Facilitates Ultrasensitive Detection of HPV Circulating Tumor DNA.

Purpose: Human papillomavirus (HPV) DNA offers a convenient circulating tumor DNA (ctDNA) marker for HPV-associated malignancies, but current methods, such as digital PCR (dPCR), provide insufficient accuracy for clinical applications in patients with low disease burden. We asked whether a next-generation sequencing approach, HPV sequencing (HPV-seq), could provide quantitative and qualitative assessment of HPV ctDNA in low disease burden settings.

Experimental Design: We conducted preclinical technical validation studies on HPV-seq and applied it retrospectively to a prospective multicenter cohort of patients with locally advanced cervix cancer (NCT02388698) and a cohort of patients with oropharynx cancer.

Liquid Biopsy Goes Viral: Next-Generation Sequencing to Enhance HPV Detection.

Liquid biopsy approaches for the detection of viral DNA can provide important information for the diagnosis and identification of virally-associated cancers. Here we discuss the next-generation sequencing-based CaptHPV method for the detection and characterization of plasma human papillomavirus (HPV) DNA in HPV-associated cancers and its potential clinical utility. See related article by Sastre-Garau et al.

Serial Cell-free DNA Assessments in Preclinical Models.

Studying circulating cell-free DNA (cfDNA) release within preclinical model systems provides opportunities to investigate the mechanisms and kinetics underlying this process under various conditions. We present a detailed protocol for longitudinal evaluation of cfDNA release through (1) seeding of cancer cell lines and establishment of xenograft tumors, (2) treatment of cancer cells and xenograft tumors, (3) serial collection of cell line media and xenograft blood, and (4) processing and isolation of cfDNA for (5) quantification of cfDNA by quantitative PCR. For complete details on the use and execution of this protocol please refer to Rostami et al.

Senescence, Necrosis, and Apoptosis Govern Circulating Cell-free DNA Release Kinetics.

The kinetics of circulating cell-free DNA (cfDNA) release may provide a real-time assessment of induced cell death. However, there is a limited understanding of the underlying biological rationale for cfDNA release following distinct treatments and cell death mechanisms. Here, we uncover a complex interplay between apoptosis, necrosis, and senescence in determining cfDNA release kinetics.

The Utility of Liquid Biopsies in Radiation Oncology.

The use of therapeutic radiation is primarily guided by clinicopathologic factors and medical imaging, whereas molecular biomarkers currently play a comparatively minor role in most settings. Liquid biopsies provide a rich source of noninvasive tumor-specific biomarkers and are amenable to repeated and noninvasive assessment. Here, we review the current status of liquid biopsies and their potential impact on the field of radiation oncology.

An Orthotopic Endometrial Cancer Model with Retroperitoneal Lymphadenopathy Made From In Vivo Propagated and Cultured VX2 Cells.

Endometrial cancer is the most common gynecologic malignancy in North America and the incidence is rising worldwide. Treatment consists of surgery with or without adjuvant therapy depending on lymph node involvement as determined by lymphadenectomy. Lymphadenectomy is a morbid procedure, which has not been shown to have a therapeutic benefit in many patients, and thus a new method to diagnose lymph node metastases is required.

Cell-free DNA as a post-treatment surveillance strategy: current status.

Circulating tumor DNA (ctDNA) consists of cell-free DNA (cfDNA) fragments that are released from tumor cells into the bloodstream. ctDNA harbors cancer-specific genetic and epigenetic alterations that allow its detection and quantification using a variety of emerging techniques. The promise of convenient non-invasive access to the complex and dynamic molecular features of cancer through peripheral blood has galvanized translational researchers around this topic with compelling routes to clinical implementation, particularly in the post-treatment surveillance setting.

Utilizing circulating tumour DNA in radiation oncology.

Emerging technologies for detection of circulating tumour DNA (ctDNA) are expanding the possibilities for clinical impact to patients with localized, potentially curable cancer. For such patients, ctDNA analysis could aid in prognostication, prediction of treatment response, longitudinal monitoring for adaptive treatment, and evaluation of minimal residual disease. Radiation oncologists currently have few tools at their disposal for predicting or rapidly assessing treatment efficacy.