Protein biomarkers and alternatively methylated cell-free DNA detect early stage pancreatic cancer

OBJECTIVE

Pancreatic ductal adenocarcinoma (PDAC) is commonly diagnosed at an advanced stage. Liquid biopsy approaches may facilitate detection of early stage PDAC when curative treatments can be employed.

DESIGN

To assess circulating marker discrimination in training, testing and validation patient cohorts (total n=426 patients), plasma markers were measured among PDAC cases and patients with chronic pancreatitis, colorectal cancer (CRC), and healthy controls. Using CA19-9 as an anchor marker, measurements were made of two protein markers (TIMP1, LRG1) and cell-free DNA (cfDNA) pancreas-specific methylation at 9 loci encompassing 61 CpG sites.

RESULTS

Comparative methylome analysis identified nine loci that were differentially methylated in exocrine pancreas DNA. In the training set (n=124 patients), cfDNA methylation markers distinguished PDAC from healthy and CRC controls. In the testing set of 86 early stage PDAC and 86 matched healthy controls, CA19-9 had an area under the receiver operating characteristic curve (AUC) of 0.88 (95% CI 0.83 to 0.94), which was increased by adding TIMP1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.06), LRG1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02) or exocrine pancreas-specific cfDNA methylation markers at nine loci (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02). In the validation set of 40 early stage PDAC and 40 matched healthy controls, a combined panel including CA19-9, TIMP1 and a 9-loci cfDNA methylation panel had greater discrimination (AUC 0.86, 95% CI 0.77 to 0.95) than CA19-9 alone (AUC 0.82; 95% CI 0.72 to 0.92).

CONCLUSION

A combined panel of circulating markers including proteins and methylated cfDNA increased discrimination compared with CA19-9 alone for early stage PDAC.

Plasma ctDNA Response Is an Early Marker of Treatment Effect in Advanced NSCLC

Plasma circulating tumor DNA (ctDNA) analysis is routine for genotyping of advanced non-small-cell lung cancer (NSCLC); however, early response assessment using plasma ctDNA has yet to be well characterized.

MATERIALS AND METHODS

Patients with advanced EGFR-mutant NSCLC across three phase I NCI osimertinib combination trials were analyzed in this study, and an institutional cohort of patients with KRAS-, EGFR-, and BRAF-mutant advanced NSCLC receiving systemic treatment was used for validation. Plasma was collected before treatment initiation and serially before each cycle of therapy, and key driver mutations in ctDNA were characterized by droplet digital polymerase chain reaction. Timing of plasma versus imaging response was compared in a separate cohort of patients with EGFR-mutant NSCLC treated with osimertinib. Across cohorts, we also studied ctDNA variability before treatment start.

RESULTS

In the NCI cohort, 14/16 (87.5%) patients exhibited ≥ 90% decrease in mutation abundance by the first on-treatment timepoint (20-28 days from treatment start) with minimal subsequent change. Similarly, 47/56 (83.9%) patients with any decrease in the institutional cohort demonstrated ≥ 90% decrease in mutation abundance by the first follow-up draw (7-30 days from treatment start). All 16 patients in the imaging cohort with radiographic partial response showed best plasma response within one cycle, preceding best radiographic response by a median of 24 weeks (range: 3-147 weeks). Variability in ctDNA levels before treatment start was observed.

CONCLUSION

Plasma ctDNA response is an early phenomenon, with the majority of change detectable within the first cycle of therapy. These kinetics may offer an opportunity for early insight into treatment effect before standard imaging timepoints.

Abstract 1374: Building an effective concordance study: Plasma Next Generation Sequencing (NGS) for oncogenic fusion detection in non-small cell lung carcinoma (NSCLC)

Background: Non-invasive genotyping of cell-free DNA (cfDNA) is increasingly used in cancer care as tumor biopsies may be inadequate or unavailable. As clinical adaptation of liquid biopsies is driven in large part by commercial vendors that offer proprietary PCR or NGS-based tests, rigorous validation of these assays is essential to ensure maximum clinical benefit. Recent efforts to compare cfDNA diagnostics have not focused on clinically actionable mutations or used tumor to verify plasma results. The present study analyzes the concordance in reports of actionable gene fusions in NSCLC from two independent, commercial plasma NGS tests, compares the breakpoint characteristics between tissue and plasma, and highlights how differences in sequencing and bioinformatic analysis can be a source of false negatives.

Methods/Results: We studied a cohort of 169 NSCLC patients (pts) that had plasma analyzed by Guardant 360 between April 2016 and July 2018. In those with tumor positive ALK, ROS1, or RET fusions (n=16), banked cfDNA from a separate tube of plasma (69% collected within 2 weeks) underwent local testing and sequencing at DFCI using Resolution Bioscience's pre-production ctDx-Lung kit with remote bioinformatic variant calling performed by Resolution Bioscience; all parties involved were blinded to tumor genotype and Guardant results. Locked results were unblinded for post hoc analysis. The ctDx-lung kit detected 13 out 16 fusions (AF% range 80-0.3%), while Guardant360 detected 7 (AF% range 10-0.3%). Guardant360 tended to report lower AFs than ctDx-lung, though corroborating TP53 alterations were of similar AFs. Of the cases where both assays did not detect any fusions, no other shared SNVs were detected, possibly due to low shed of tumor DNA. Of the 13 cases where a fusion was detected in plasma by ctDx-lung, 4 rearrangements could be characterized as ‘non-productive’ due to opposite transcriptional orientations and comprised 50% (3/6) of the fusions not detected by Guardant360. Only one case detected by Guardant360 was ‘non-productive’. Of the 13 cases where a fusion was detected in plasma, 89% (8/9) of pts with productive fusions and 75% of pts (3/4) with ‘non-productive’ fusions responded to TKI therapies. Additional unblinding is ongoing to better understand false negative cases.

Conclusions: Here, we demonstrate that a rigorous approach to benchmarking plasma genotyping assays should 1) focus on actionable mutations, 2) use tumor as a gold standard for establishing true and false positives and negatives, and 3) include orthogonal validation to address assay design and bioinformatic analyses as sources of discordance. Our study further highlights the challenges of fusion detection and interpretation and the need for platform cross-comparisons to realize the potential of liquid biopsy to increase access to personalized cancer care.

Citation Format: Julianna G. Supplee, Marina S. Milan, Kristy T. Potts, Lynette M. Sholl, Tristan S. Shaffer, Lee P. Lim, Pasi A. Janne, Geoffrey R. Oxnard, Cloud P. Paweletz. Building an effective concordance study: Plasma Next Generation Sequencing (NGS) for oncogenic fusion detection in non-small cell lung carcinoma (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1374.

Salivary HPV DNA informs locoregional disease status in advanced HPV-associated oropharyngeal cancer

OBJECTIVES

Quantifying tumor DNA in tissue and circulating in blood permits high-quality molecular monitoring to detect and track cancer progression. Evaluating tumor DNA in both blood and saliva in human papillomavirus (HPV)-associated oropharyngeal cancer (OPC) could provide a non-invasive and clinically actionable method for real-time disease detection.

METHODS

We previously validated an ultrasensitive droplet-digital (dd)PCR assay targeting the dominant high-risk HPV subtypes causally linked to OPC. Here we enrolled an observational cohort to evaluate the predictive and prognostic potential of paired plasma-salivary tumor DNA among 21 patients with advanced HPV+OPC.

RESULTS

In patients with recurrent, persistent locoregional (LR) disease, median baseline normalized salivary HPV DNA was 10.9 copies/ng total DNA, nearly 20x higher compared with those with distant disease only (p = 0.01). A cutoff of 5 copies/ng yielded 87% sensitivity and 67% specificity for accurately predicting LR disease. Total tumor burden among those with LR disease strongly correlated with salivary HPV DNA levels (R = 0.83, p = 0.02). The rise and fall of salivary HPV DNA predicted treatment failure and response, respectively, in all patients with LR disease, and predated imaging findings. Among paired salivary-plasma (cell-free) cfDNA samples, only higher plasma HPV cfDNA levels were associated with poor outcomes (p < 0.01), suggesting that each bodily fluid provides unique information about HPV disease status.

CONCLUSIONS

Salivary HPV DNA provides valuable information about tumor burden and predicts treatment response in advanced HPV+OPC. Paired blood-saliva samples could be used to monitor HPV DNA with broad applications to inform diagnosis, prognosis, and surveillance in HPV-associated diseases.

Abstract 2581: Plasma HPV cell free DNA as an earlier predictor of treatment response in advanced oropharyngeal cancer

Purpose: Human papillomavirus (HPV) is associated with the majority of oropharyngeal squamous cell carcinomas (OPSCC), with a rising incidence of OPSCC predominantly among middle-aged men. Tumor-derived HPV cell-free (cf)DNA can be detected and quantified in circulation with high sensitivity and specificity. Although cfDNA has limited clinical application in monitoring locoregional spread of these tumors, up to 10% of HPV+ OPSCC patients present or recur with distant, metastatic disease. The potential of HPV DNA monitoring in this setting remains largely unexplored.

Methods: We present a proof-of-concept prospective observational cohort of recurrent, metastatic (R/M) HPV+ OPSCC patients treated with standard systemic therapies. We utilized droplet digital (dd)PCR to identify and quantify HPV cfDNA (strains 16, 18, 31, 33 and 45) at multiple time points throughout treatment. We then compared HPV cfDNA concentration at various timepoints with clinical parameters such as disease burden and treatment response.

Results: Clinicopathologic data from 12 R/M patients revealed a predominantly male cohort (11/12, 92%) with a median age of 55 at diagnosis. Eight (67%) were on immunotherapy treatments and the other four on standard chemotherapy during the study period (2.5 months). Plasma HPV cfDNA was detected in 6/12 (50%) samples (range 0-4460 copies/mL) in at least one timepoint during the study. All patients with undetectable HPV cfDNA had evidence of stable, low burden disease or no measurable lesions (near-complete response) on their current therapy. HPV cfDNA levels strongly correlated with both disease burden (p &lt; 0.01) and distant disease sites (p &lt; 0.01). In three cases, HPV DNA levels declined prior to contrast enhanced imaging findings which later confirmed treatment response (up to 14 days prior to planned imaging).

Conclusion: Our results suggest that high sensitivity plasma HPV cfDNA levels can be an early indicator of treatment response. HPV cfDNA monitoring could significantly impact clinical decision-making and improve patient outcomes by informing treatment response or failure. Further studies are underway to validate these findings and determine how early cfDNA can detect metastatic disease.

Citation Format: Glenn J. Hanna, Julianna G. Supplee, Yanan Kuang, Kate Geary, Pasi A. Janne, Robert I. Haddad, Cloud P. Paweletz. Plasma HPV cell free DNA as an earlier predictor of treatment response in advanced oropharyngeal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2581.