Investigator
Princess Margaret Cancer Centre
Combined Transcriptome and Circulating Tumor DNA Longitudinal Biomarker Analysis Associates With Clinical Outcomes in Advanced Solid Tumors Treated With Pembrolizumab
PURPOSE Immune gene expression signatures are emerging as potential biomarkers for immunotherapy (IO). VIGex is a 12-gene expression classifier developed in both nCounter (Nanostring) and RNA sequencing (RNA-seq) assays and analytically validated across laboratories. VIGex classifies tumor samples into hot, intermediate-cold (I-Cold), and cold subgroups. VIGex-Hot has been associated with better IO treatment outcomes. Here, we investigated the performance of VIGex and other IO biomarkers in an independent data set of patients treated with pembrolizumab in the INSPIRE phase II clinical trial (ClinicalTrials.gov identifier: NCT02644369 ). MATERIALS AND METHODS Patients with advanced solid tumors were treated with pembrolizumab 200 mg IV once every 3 weeks. Tumor RNA-seq data from baseline tumor samples were classified by the VIGex algorithm. Circulating tumor DNA (ctDNA) was measured at baseline and start of cycle 3 using the bespoke Signatera assay. VIGex-Hot was compared with VIGex I-Cold + Cold and four groups were defined on the basis of the combination of VIGex subgroups and the change in ctDNA at cycle 3 from baseline (ΔctDNA). RESULTS Seventy-six patients were enrolled, including 16 ovarian, 12 breast, 12 head and neck cancers, 10 melanoma, and 26 other tumor types. Objective response rate was 24% in VIGex-Hot and 10% in I-Cold/Cold. VIGex-Hot subgroup was associated with higher overall survival (OS) and progression-free survival (PFS) when included in a multivariable model adjusted for tumor type, tumor mutation burden, and PD-L1 immunohistochemistry. The addition of ΔctDNA improved the predictive performance of the baseline VIGex classification for both OS and PFS. CONCLUSION Our data indicate that the addition of ΔctDNA to baseline VIGex may refine prediction for IO.
Circulating human papillomavirus DNA sequencing as a biomarker of response in advanced cervical cancer
Despite intense multi-modal treatment, the prognosis for advanced cervical cancer remains poor. The recent increase in cervical cancer cases worldwide highlights an urgent need for clinically validated biomarkers to guide patient management. Our pilot study investigates the utility of human papillomavirus (HPV) circulating tumor deoxy ribonucleic acid (ctDNA) in metastatic and recurrent cervical cancer. We investigated the association of HPV ctDNA levels, early kinetics, and detection of viral-host integration sites with response and outcomes. Serial plasma samples were prospectively collected from 21 patients with metastatic/recurrent cervical cancer. HPV ctDNA genotyping and quantification were conducted using a previously validated hybrid capture next-generation sequencing-based method. Mutation profiles within ctDNA were investigated simultaneously using a bespoke panel. In addition, high-confidence HPV integration was detected and quantified in ctDNA using SearcHPV. Differences in progression-free survival and overall survival were also evaluated between patients with high-confidence integration sites detected at baseline and those with low or no-confidence integration sites using the Kaplan-Meier method and log-rank tests to compare groups. This pilot study cohort included 21 patients with HPV-associated cervical cancer. Treatments included front-line platinum-based chemotherapy without (n = 4) or with (n = 5) bevacizumab, bevacizumab monotherapy (n = 2), or subsequent therapy (n = 7). A total of 3 previously treated patients were included to study HPV kinetics during observation. At baseline, HPV ctDNA was detected in 20 of 21 patients (95.2%). From baseline to the first assessment, a change in HPV ctDNA was significantly associated with type of response in patients on treatment (n = 18) (p = .049) and across all patients (n = 21) (p = .008). A total of 26 unique mutations were detected in either plasma or tissue. Of these, 11 of 26 were only detected in plasma, 9 of 26 were only detected in tissue, and 6 of 26 were detected in plasma and tissue. Patients with a high-confidence HPV integration site detected within ctDNA at baseline have inferior overall survival compared with patients with low-confidence or undetectable integration. In this pilot study, a decrease in HPV ctDNA was associated with response to treatment in metastatic and recurrent cervical cancer. HPV site integration and mutation-based ctDNA may have application to personalized therapy and should be evaluated in larger studies.
Clinical Validation of Human Papilloma Virus Circulating Tumor DNA for Early Detection of Residual Disease After Chemoradiation in Cervical Cancer
PURPOSE Most cervical cancers are caused by human papilloma virus (HPV), and HPV circulating tumor DNA (ctDNA) may identify patients at highest risk of relapse. Our pilot study using digital polymerase chain reaction (dPCR) showed that detectable HPV ctDNA at the end of chemoradiation (CRT) is associated with inferior progression-free survival (PFS) and that a next-generation sequencing approach (HPV-seq) may outperform dPCR. We aimed to prospectively validate HPV ctDNA as a tool for early detection of residual disease. METHODS This prospective, multicenter validation study accrued patients with stage IB-IVA cervical cancer treated with CRT between 2017 and 2022. Participants underwent phlebotomy at baseline, end of CRT, 4-6 weeks post-CRT, and 3 months post-CRT for HPV ctDNA levels. Plasma HPV genotype–specific DNA levels were quantified using both dPCR and HPV-seq. The primary end point was 2-year PFS. RESULTS With a median follow-up of 2.2 (range, 0.5-5.5) years, there were 24 PFS events among the 70 patients with HPV+ cervical cancer. Patients with detectable HPV ctDNA on dPCR at the end of CRT, 4-6 weeks post-CRT, and 3 months post-CRT had significantly worse 2-year PFS compared with those with undetectable HPV ctDNA (77% v 51%, P = .03; 82% v 15%, P < .001; and 82% v 24%, P < .001, respectively); the median lead time to recurrence was 5.9 months. HPV-seq showed similar results as dPCR. On multivariable analyses, detectable HPV ctDNA on dPCR and HPV-seq remained independently associated with inferior PFS. CONCLUSION Persistent HPV ctDNA after CRT is independently associated with inferior PFS. HPV ctDNA testing can identify, as early as at the end of CRT, patients at high risk of recurrence for future treatment intensification trials.
FDG-PET and Circulating HPV in Patients With Cervical Cancer Treated With Definitive Chemoradiation (II)
Nearly all cervical cancers are caused by the human papilloma virus (HPV), which can be detected in cancer tissue by laboratory tests. There is evidence that the virus can also be detected from a blood sample to monitor the effects of treatment. Previous studies have shown that a special test called 18F-Fluorodeoxyglucose (FDG) Positron Emission Tomography/Computed Tomography (PET-CT) at 3 months after treatment may predict survival in cervical cancer. The purpose of this study is to see how well the FDG-PET Scan and blood tests for HPV can detect leftover cervical cancer cells after treatment. This study is not a particular form of treatment and patients will receive standard of care treatment.
Liquid Biopsy Evaluation and Repository Development at Princess Margaret
The objective of this protocol is to develop an institution-wide liquid biopsy protocol that will establish a common process for collecting blood and corresponding archived tumor specimens for future research studies at the University Health Network's Princess Margaret Cancer Centre. Circulating cell-free nucleic acids (cfNA), including cell-free DNA (cfDNA) and cell-free RNA (cfRNA), are non-invasive, real-time biomarkers that can provide diagnostic and prognostic information before cancer diagnosis, during cancer treatment, and at disease progression. Cancer research scientists and clinicians at the Princess Margaret are interested in incorporating the collection of peripheral blood samples ("liquid biopsies") into research protocols as a means of non-invasively assessing tumor progression and response to treatment at multiple time points during a patient's course of disease.
Study of the Effects of Pembrolizumab in Patients With Advanced Solid Tumors
This is a phase 2 study whose main purpose is to evaluate gene changes and immune biomarkers in patients with solid tumors during treatment with pembrolizumab and in relation to response to treatment. Pembrolizumab is a monoclonal antibody that is designed to block a protein called programmed cell death 1 ligand 1 (PD-L1) which will allow the body's immune system to kill the cancer cells.
