Abstract B028: Changes in exosomal RNA expression associate with treatment response to BRAF + EGFR + PD-1 blockade in MSS, BRAFV600E colorectal cancer: A liquid biopsy approach
Authors: Morris Van Karlyle , Rajapakshe Kimal I. , Bahrambeigi Vahid , Parsehgian Christine M. , Johnson Benny , Raghav Kanwal P. , Dasari Arvind , Huey Ryan W. , Overman Michael J. , Willis Jason , Lee Michael S. , Wolff Robert A. , Kee Bryan K. , Le Phat , Guerrero Paola A. , Kopetz Scott , Maitra Anirban 
Published: December 2022

Abstract
Introduction: BRAF + EGFR inhibition induces decreased expression of mismatch repair (MMR) genes in preclinical models of microsatellite stable (MSS), BRAFV600E metastatic colorectal cancer (mCRC) but has not been reported in patients. We evaluated exosomal RNA (exoRNA) isolated from serial blood specimens collected from patients (pts) with MSS, BRAFV600E mCRC treated with encorafenib (E) + cetuximab (C) + nivolumab (N) as a novel blood-based approach to compare differences in gene expression according to treatment response. Methods: Pts with refractory MSS, BRAFV600E mCRC were treated with E (300 mg daily), C (500 mg/m2 q2 weeks), and N (480 mg q4 weeks) on an IRB-approved clinical trial at MD Anderson. Responses to treatment were assessed every 8 weeks (RECIST v1.1). ExoRNA isolated from pretreatment and on-treatment (week 8) blood samples were sequenced (SMART-seq) and deconvoluted (DeMix) in order to estimate cancer-specific gene expression. Previously validated MAPK and interferon (IFN)-γ gene expression signatures were used for measuring transcriptomic changes following treatment with E+C+N. Scores between responders and non-responders were compared by unpaired t-tests. For Gene Set Enrichment Analysis (GSEA), an adjusted false discovery rate (FDR) &lt; 0.25 was applied to find significantly enriched pathways between on-treatment and pretreatment samples separately for responders and non-responders. Results: 26 pts were treated with E+C+N, and 24 were evaluable for response. Overall response rate was 50% (95% confidence interval (CI), 29-71), and median progression-free survival was 7.4 months (95% CI, 6.0-NA). Four pts remained on study &gt; 12 months. Between responders vs non-responders (N=12 each), mean changes in MAPK signature score was decreased (-0.63 vs 0.15, respectively; p=.13). Both patients with response &gt; 18 months demonstrated dramatic increases in IFN-γ score following treatment with E+C+N (+13.1 and +14.6), a trend not observed in all other patients (range, -18.0 to 3.6). Among responders to E+C+N, GSEA analysis demonstrated dynamic pathway changes in normalized enrichment score (NES) for DNA repair (NES -2.3; p-adj=.008), IL6/JAK/STAT3 (NES -2.1, p-adj=.02), and IFN-α response (NES -2.0, p-adj=.03). For non-responders, relative increases in NES were observed for angiogenesis (NES 2.1, p-adj=.02) and IL-2/STAT5 (NES 2.0, p-adj= .02). Conclusions: Transcriptome analysis using exoRNA isolated from serial blood samples is feasible for assessing treatment response in pts with mCRC. Decreased MAPK score in exoRNA may be associated with treatment response to E+C+N in pts with MSS, BRAFV600E mCRC. Changes in immune NES scores following treatment may distinguish responders from non-responders to MAPK + PD-1 blockade and highlight targets for novel immune-mediated combinations for MSS, BRAFV600E mCRC.
Citation Format: Van Karlyle Morris, Kimal I. Rajapakshe, Vahid Bahrambeigi, Christine M. Parsehgian, Benny Johnson, Kanwal P. Raghav, Arvind Dasari, Ryan W. Huey, Michael J. Overman, Jason Willis, Michael S. Lee, Robert A. Wolff, Bryan K. Kee, Phat Le, Paola A. Guerrero, Scott Kopetz, Anirban Maitra. Changes in exosomal RNA expression associate with treatment response to BRAF + EGFR + PD-1 blockade in MSS, BRAFV600E colorectal cancer: A liquid biopsy approach [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr B028.