Abstract 5870: Taxane-based chemotherapy leads to acquired resistance through ecDNA-based amplification of multi-drug resistance genes
Authors: Holmes Kristen , Perusse Dean , DuPai Cory , Hemmati Homa , Weiss Julie , Kuelbs Claire , Bibay John , Chen Joan , Liao Debbie , Hassig Christian , Kasibhatla Shailaja 
Published: March 2024

Abstract
Focal amplification on extrachromosomal DNA (ecDNA) drives high gene copy number and intercellular genomic heterogeneity, which can fuel tumor adaptation and drug resistance. Targeted therapies have largely failed in patients with oncogene amplification, and patients whose tumors harbor ecDNA-based gene amplification have particularly worse survival compared to patients whose cancers harbor other genetic drivers. Due to the lack of approved therapies for patients with oncogene amplified cancers, many patients receive chemotherapy; however, resistance often develops through mechanisms such as ATP-binding cassette (ABC) transporter overexpression, rendering cross-resistance to other forms of chemotherapy. We examined whether ecDNA amplification in tumor cell lines drives ABC transporter overexpression to mediate resistance to paclitaxel, a commonly prescribed taxane chemotherapy for cancer patients.
We selected non-amplified (DLD1 and SW48) and amplified cell lines, including COLO320DM and COLO320HSR (MYC amplified on ecDNA or chromosomal loci, respectively); SNU16 and H716, (FGFR2 and MYC amplified ecDNA); and H2170 (ERBB2 and MYC amplified on ecDNA). All cell lines developed paclitaxel resistance, with the majority (5/7) gaining focal amplification of ABCB1, which encodes P-glycoprotein (P-gp), a common multi-drug resistance transporter. Four models–COLO320DM, COLO320HSR, SNU16, and H2170—developed ABCB1 amplification on ecDNA; one non-amplified cell line (DLD1) acquired focal ABCB1 amplification via a breakage-fusion-bridge (BFB) mechanism, a distinct form of amplification from ecDNA. ecDNA-based ABCB1 amplifications exhibited hallmarks of ecDNA, including intercellular copy number heterogeneity and paclitaxel dose-dependent rapid evolution of ABCB1 copy number.
We next assessed whether drug resistance was reversible in ABCB1 amplified cell lines following removal of paclitaxel. Reversal of resistance was observed in COLO320DM and COLO320HSR via loss of ABCB1 ecDNA within 4-6 weeks. However, in SNU16 and H2170 resistant cells, ABCB1 amplification was retained up to 12 weeks of drug removal, with apparent integration into MYC ecDNA, demonstrating that ecDNA-enabled plasticity can result in both short- and long-term paclitaxel resistance.
Although targeted therapies have revolutionized treatment approaches for patients with actionable oncodriver alterations, most cancer patients do not have actionable drivers and most patients still receive chemotherapy at some point in their course of treatment. We demonstrated that ecDNA-based resistance to paclitaxel is common in cancer cell lines and may also drive resistance to chemotherapy in patients. Thus, ecDNA-directed therapies (ecDTx) may be an important treatment option for chemo-resistant patients, who currently do not have many effective therapeutic options.
Citation Format: Kristen Holmes, Dean Perusse, Cory DuPai, Homa Hemmati, Julie Weiss, Claire Kuelbs, John Bibay, Joan Chen, Debbie Liao, Christian Hassig, Shailaja Kasibhatla. Taxane-based chemotherapy leads to acquired resistance through ecDNA-based amplification of multi-drug resistance genes [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 5870.