The role of liquid biopsy in management of the neck with indeterminate response on post-treatment imaging following non-surgical management of oropharyngeal cancer

INTRODUCTION

This study aimed to determine if post-treatment HPV cell-free DNA (cfDNA) can assist in the decision-making process for salvage neck dissection in patients following non-surgical treatment of oropharyngeal squamous cell carcinoma (OPSCC) with a partial response in the neck on imaging at 12 weeks post-treatment.

METHODS

86 patients who completed treatment were prospectively recruited through the regional multidisciplinary team (MDT). Treatment response was categorised as complete response (CR), partial response (PR) or progressive disease on 12-week post-treatment imaging. Pre- and post-treatment blood samples were assessed for HPV cfDNA through droplet digital PCR (ddPCR).

RESULTS

Eight patients had an isolated partial response in the neck. One (12.5%) had detectable HPV cfDNA (22.96 copies/ml) at ∼12 weeks post-treatment with positive disease on subsequent neck dissection (positive predictive value; PPV = 100%). Of the seven patients with undetectable HPV cfDNA, two patients had evidence of regional disease recurrence at 23.9 and 27.4 months respectively (negative predictive value; NPV = 71%).

CONCLUSION

The detection of HPV cfDNA may help target salvage therapy in patients with a partial response in the neck. Follow-up studies in larger cohorts would be required to further validate the use of post-treatment HPV cfDNA in the management of OPSCC.

Abstract 3408: Longitudinal measurement of HPV copy number in cell free DNA predicts progression free survival in HPV positive oropharyngeal cancer

Oropharyngeal squamous cell carcinoma (OPSCC) is increasing in global prevalence and is divided into two types dependent on association with human papillomavirus (HPV), with a more favorable prognosis in HPV+ve tumors. Assay of HPV copy number in plasma cell-free DNA (cfDNA) provides a minimally invasive method for detecting and monitoring tumor-derived HPV, with potential for enhancing clinical care. We have evaluated the utility of cfDNA droplet digital PCR (ddPCR) as a method for characterisation and longitudinal monitoring of patients with OPSCC in a prospectively recruited cohort of 104 OPSCC patients. ddPCR assay of cfDNA for five HPV types showed overall 95% concordance with p16 immunohistochemistry (IHC) and PCR analysis of solid tumor tissue. Longitudinal sampling in 48 HPV+ve patients, with median follow-up of 20 months, strongly predicted patient outcomes. Progression-free survival, stratified respectively by the presence or absence of detectable HPV cfDNA at a median of 13 weeks post-treatment, was 50% and 88% (p=0.001, hazard ratio 10.0 (95% CI 2.1-47.1)). In two patients, greater reliance on sequential HPV measurement would have avoided surgical intervention which ultimately did not confirm disease recurrence. The high concordance of pre-treatment plasma cfDNA-HPV analysis with p16 IHC and HPV-PCR of solid tissue, together with the predictive value and utility of sequentially measured post-treatment cfDNA-HPV copy number, provide a compelling case for the routine use of cfDNA-HPV ddPCR in management of OPSCC and for clinical trials to assess its impact on treatment outcomes.

Citation Format: Martyna Joanna Adamowicz, Sophie J. Warlow, John P. Thomson, Lara M. Carey, Helen Thain, Robert Wescott, Kate Cuschieri, Lucy Q. Li, Brendan Conn, Ashley Hay, Iain J. Nixon, Timothy J. Aitman. Longitudinal measurement of HPV copy number in cell free DNA predicts progression free survival in HPV positive oropharyngeal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3408.

Longitudinal measurement of HPV copy number in cell-free DNA is associated with patient outcomes in HPV-positive oropharyngeal cancer

INTRODUCTION

Oropharyngeal squamous cell carcinoma (OPSCC) is increasing in global prevalence and is divided into two types dependent on association with human papillomavirus (HPV). Assay of HPV copy number in plasma cell-free DNA (cfDNA) provides a minimally invasive method for detecting and monitoring tumour-derived HPV, with potential for enhancing clinical care.

MATERIALS AND METHODS

In a prospectively recruited cohort of 104 OPSCC patients, we evaluate the utility of cfDNA droplet digital PCR (ddPCR) as a method for characterisation and longitudinal monitoring of patients with OPSCC.

RESULTS

ddPCR assay of pre-treatment plasma cfDNA for five HPV types showed overall 95% concordance with p16 immunohistochemistry and PCR analysis of tumour tissue. Longitudinal sampling in 48 HPV+ve patients, with median follow-up of 20 months, was strongly associated with patient outcomes. Persistently elevated cfDNA-HPV post-treatment was associated with treatment failure (2/2 patients) and an increase of cfDNA-HPV in patients whose HPV levels were initially undetectable post-treatment was associated with disease recurrence (5/6 patients). No recurrence was observed in patients in whom cfDNA-HPV was undetectable in all post-treatment samples. In two patients, sequential HPV measurement could have avoided surgical intervention which did not confirm recurrence.

CONCLUSION

The high concordance of pre-treatment plasma cfDNA-HPV analysis with tissue-based assays, together with the clinical associations of sequentially measured post-treatment cfDNA-HPV copy number add to a growing body of evidence that suggest utility of cfDNA-HPV ddPCR in management of OPSCC. Standardised clinical trials based on these data are now needed to assess the impact of such testing on overall patient outcomes.

Abstract A02: Detection of circulating cell-free DNA in renal cancer using renal cancer-specific DNA mutations and methylation changes

Renal cell cancer (RCC) is the most deadly of urologic malignancies. It is a very invasive and chemoresistant disease that is often treated by surgical resection as it also responds poorly to radiotherapy. Importantly, more than 30% of RCCs recur or metastasize following treatment and in the cases believed to be curable by nephrectomy, distant metastasis can develop even 10 years post-surgery. There is therefore a significant focus on tissue-based biomarkers from the primary kidney tumors to help predict which patients are likely to recur, though there are no biomarkers used in routine clinical practice. Over recent years, much research has aimed at the utilization of blood-based biomarkers, mainly circulating cell-free DNA (cfDNA), as a method of noninvasive disease diagnosis and monitoring. cfDNA is detected through the identification of tumor-specific cfDNA mutations, although cfDNA methylation may be a more specific biomarker as many CpG sites can be tested in parallel. We have collected tumor tissue and pre- and post-surgery blood samples from renal cancer patients and generated exome sequencing and EPIC array data of 20 tumors with matched blood samples to detect tumor-specific DNA mutations and methylation patterns. We have identified well-known driver mutations in renal cancer in VHL in 11 tumors at 0.12-0.51 variant allele fraction (VAF); PBRM1 in 8 tumors at 0.12-0.45 VAF; BAP-1 in 2 tumors at 0.45 and 0.3 VAF; and SETD2 at 0.39 VAF; KDM5C at 0.27 VAF, and CTNNA2 at 0.2 VAF in one out of 20 patients. We aim to validate these changes using droplet digital PCR (ddPCR) in tumor and circulating tumor DNA (ctDNA) pre- and post-surgery. We next plan to combine the result of the exome sequencing with EPIC array data as well in house-developed cfDNA profiles based on publicly available tissue and individual cell type DNA methylation data. This approach will allow us to select the best mutation and methylation diagnostic and prognostic markers to aid the monitoring of early disease and relapse as well as the treatment of renal cell cancer.

Citation Format: Martyna J. Adamowicz, John Thomson, Sophie J. Warlow, Utsa Patra, Helen Thain, Sophie Marion de Proce, Alexander Laird, Timothy J. Aitman. Detection of circulating cell-free DNA in renal cancer using renal cancer-specific DNA mutations and methylation changes [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A02.