Abstract 5584: Analysis of cell free DNA to predict outcome to Bevacizumab combination therapy in metastatic colorectal cancer patients
Authors: Miller Ian S. , Thomas Valentina , Venken Tom , Arijs Ingrid , Barat Ana , Betge Johannes , Zhan Tianzuo , Gaiser Timo , Ebert Matthias P. , Prehn Jochen , Klinger Rut , O’Connor Darran P. , Moulton Brian Brian , Murphy Verena , McDermott Ray , Bird Brian , Leonard Gregory , Grogan Liam , Horgan Anne , Schulte Nadine , Moehler Markus , Prannikar Nicole , Franz-Werner Judith , Feustel Hans-Peter , Lambrechts Diether , Byrne Annette T. 
Published: April 2023

Abstract
Purpose: Cell-free DNA (cfDNA) analysis in plasma is an emerging technique with numerous applications in oncology. We employed cfDNA to determine chromosomal instability (CIN), nucleosome footprints (NF) and methylation profiles in metastatic colorectal cancer (mCRC) patients and to predict outcome to bevacizumab (BVZ) combination therapy.
Experimental Design: Low coverage whole-genome sequencing (LC-WGS) was performed on matched tumor and plasma samples from 74 mCRC patients participating in the CTRIAL-IE 12-16 AC-ANGIOPREDICT Phase II clinical trial (NCT01822444), prior to receiving BVZ, and analyzed for CIN (3 subclusters with low, intermediate and high CIN, respectively) and nucleosomes. For 61/74 mCRC patients, plasma samples before and after BVZ treatment were available and used for targeted methylation sequencing. A validation cohort of mCRC plasma samples (n= 24) from the University Medical Center Mannheim (UMM) was similarly profiled.
Results: Based on cfDNA CIN profiles, we subtyped mCRC patients with 92.3% accuracy of sample distinction into low and high CIN clusters (cluster 1 against cluster 2 and 3), demonstrating concordance between matched plasma and tumor samples. Improved survival outcome was observed in CIN high patients. Plasma-based CIN clustering and improved survival for CIN high patients was also confirmed in the UMM cohort. NF and methylation profiles differed between CIN clusters and healthy individuals, and could reliably separate cluster 1 from cluster 2 and 3 samples (AUC=0.72 and 0.85 respectively). A large methylation score decrease after BVZ treatment was associated with improved overall survival (p = 0.013).
Conclusions: cfDNA can be analyzed to predict outcome to BVZ in mCRC patients. Detection of CNAs, NFs and methylation profiles facilitated stratification of samples into CIN clusters and informed patient response to treatment.
Citation Format: Ian S. Miller, Valentina Thomas, Tom Venken, Ingrid Arijs, Ana Barat, Johannes Betge, Tianzuo Zhan, Timo Gaiser, Matthias P. Ebert, Jochen Prehn, Rut Klinger, Darran P. O’Connor, Brian Brian Moulton, Verena Murphy, Ray McDermott, Brian Bird, Gregory Leonard, Liam Grogan, Anne Horgan, Nadine Schulte, Markus Moehler, Nicole Prannikar, Judith Franz-Werner, Hans-Peter Feustel, Diether Lambrechts, Annette T. Byrne. Analysis of cell free DNA to predict outcome to Bevacizumab combination therapy in metastatic colorectal cancer patients. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5584.