Abstract 2422: Liquid biopsy approaches for monitoring metastatic pancreatic cancer in immunotherapy treated patients
Authors: Hruban Carolyn Anna , Chen Inna , Bruhm Daniel C. , Koul Shashikant , Yao Jennie , Theile Susann , Boyapati Kavya , Vulpescu Nicholas A. , Annapragada Akshaya , Ferreira Leonardo , Cristiano Stephen , Foda Zachariah H. , Adleff Vilmos , Johansen Julia , Phallen Jillian , Scharpf Robert B. , Velculescu Victor E. 
Published: March 2024

Abstract
Introduction: Pancreatic cancer has a poor prognosis especially when identified at advanced stages. Globally in 2020, &gt;450,000 people died from the disease. For those with locally advanced or metastatic cancer, the standard of care treatment is chemotherapy. Preliminary studies show that some patients with advanced-stage disease respond to immune checkpoint blockade treatment. Determining response to therapy using imaging techniques can be challenging. There is a clinical unmet need for noninvasive approaches that can provide a real-time assessment of response to therapy in these patients. We evaluated two methods for assessing response to therapy using circulating cell-free DNA (cfDNA) in patients with metastatic pancreatic cancer treated with immune checkpoint inhibition and radiation as part of the CheckPAC study (NCT02866383).
Methods: For all patients with available samples (n=40), we evaluated one pre-treatment blood draw and one on-treatment blood draw (26-65 days after treatment start). We extracted cfDNA from each sample and performed low-coverage 1-2x whole genome sequencing (WGS). We evaluated tumor and matched buffy coat for the 34 patients who had &gt; 10% tumor purity using WGS with at least 60x and 30x coverage, respectively. We compiled the mutated bases in the tumor genome and examined these positions in the cfDNA. We counted the number of mutant observations from cfDNA WGS and divided them by the total number of observations at these bases to calculate whole-genome mutant allele frequency (MAF). We categorized responders based on &gt;30% drop in MAF from baseline. In a tissue independent approach, we detected changes in genome-wide cfDNA fragmentation patterns using the DNA evaluation of fragments for early interception (DELFI) approach. We evaluated survival using DELFI scores of on-treatment samples. Samples were designated DELFI high (above median) or DELFI low (below median.) Log-Rank tests were used to compare survival curves.
Results: For the mutation based approach, molecular responders (n=7) had a median progression free survival (PFS) of 485 days compared to 57 days for non-responders (n=9) (p=0.02). Molecular responders had a median overall survival (OS) of 694 days compared to 200 days for non-responders (p=0.062). Patients with DELFI low scores after therapy (n=14) had a longer median PFS than those with DELFI high scores (n=14) (307 days versus 70 days, respectively) (p=0.013). DELFI low patients also had a longer median OS than DELFI high patients (627 vs 158 days, respectively) (p&lt;0.0001).
Conclusions: These analyses suggest that WGS mutation-based and fragmentation cfDNA approaches can identify individuals with metastatic pancreatic cancer who respond to immune checkpoint inhibition. Incorporation of these molecular methods for evaluation of tumor burden may provide information for patient-physician decision making to improve patient quality of life.
Citation Format: Carolyn Anna Hruban, Inna Chen, Daniel C. Bruhm, Shashikant Koul, Jennie Yao, Susann Theile, Kavya Boyapati, Nicholas A. Vulpescu, Akshaya Annapragada, Leonardo Ferreira, Stephen Cristiano, Zachariah H. Foda, Vilmos Adleff, Julia Johansen, Jillian Phallen, Robert B. Scharpf, Victor E. Velculescu. Liquid biopsy approaches for monitoring metastatic pancreatic cancer in immunotherapy treated patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2422.