Abstract 5707: Tumor and immune determinants of response to anti-BCMA CAR T-cell therapy in multiple myeloma using cell-free DNA
Authors: Carleton Mia , Hosoya Hitomi , Tanaka Kailee L. , Sworder Brian , Hovanky Vanna , Sahaf Bita , Frank Matthew J. , Duran George E. , Zhang Tian Y. , Arai Sally , Iberri David , Liedtke Michaela , Miklos David B. , Khodadoust Michael S. , Sidana Surbhi , Kurtz David M. 
Published: April 2023

Abstract
Background: Multiple myeloma (MM) is an incurable disease with a heterogenous clinical course and genomic landscape. Autologous anti-BCMA chimeric antigen receptor (CAR) T-cells are a promising new therapy, but determinants of response and resistance are not well known. Cell-free DNA (cfDNA) is a useful tool to study MM as it allows for repeated, non-invasive tumor assessment. We apply a novel method for simultaneously tracking tumor mutations and CAR T-cells from cfDNA using Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq).
Methods: We designed a 480kb CAPP-Seq hybrid capture panel to identify mutations, track tumor burden and minimal residual disease, and detect cfDNA derived from the CAR transgene (CAR-cfDNA) in patients receiving idecabtagene vicleucel (ide-cel). Flow cytometry (FC) for enumeration of CAR T-cells was performed from peripheral blood mononuclear cells (PBMCs) when available.
Results: We profiled 153 biologic samples, including plasma, PBMCs, and bone marrow mononuclear cells, from 15 patients receiving ide-cel and 18 healthy controls. We observed a median of 84 SNVs (range 30-277) prior to therapy. Patients with prolonged responses (&gt;90 days) had significantly lower circulating tumor DNA (ctDNA) at day 28 post-infusion than patients with early progression (&lt;90 days) (0.6 vs. 4.6 log haploid genome equivalents (hGE)/mL; p=0.002). Additionally, higher ctDNA at D28 was prognostic for time to progression (TTP) (HR=1.67, p=0.019). We validated CAR-cfDNA detection by comparison with FC from PBMCs at matched timepoints (n=38), finding a significant correlation (rho=0.79, p=3E-09). CAR-cfDNA typically reached its peak level around D14 (median 332 hGE/mL), with ctDNA declining at the same time-point. Thus, CAR-cfDNA levels and ctDNA burden were inversely correlated (rho= -0.3, p=0.019). Surprisingly, peak CAR expansion was not associated with TTP (HR=1, p=0.463). However, lower CAR-cfDNA at D28 was prognostic for inferior TTP (HR=2.68, p=0.011). This suggests CAR persistence may play a more important role in clinical outcomes. Furthermore, among progressors, time until loss of detectable CAR-cfDNA correlated with TTP (rho=0.81, p=0.02). Patients who progressed before day 90 had a median CAR persistence of 28 days. In contrast, patients who progressed after day 90 had a median of 137 days and often had emergent copy number alterations in ctDNA at relapse. This included one case with emergent loss of chr16, where TNFRSF17 (BCMA), resides. This event was detected 36 days prior to clinical relapse; BCMA loss was validated via whole-genome sequencing and immunohistochemistry staining of the tumor.
Conclusions: Cell-free DNA is a promising biomarker for mutational genotyping, disease monitoring, and tracking CAR T-cells in MM. The persistence of CAR-cfDNA has particular prognostic importance and novel strategies to increase CAR persistence should be explored.
Citation Format: Mia Carleton, Hitomi Hosoya, Kailee L. Tanaka, Brian Sworder, Vanna Hovanky, Bita Sahaf, Matthew J. Frank, George E. Duran, Tian Y. Zhang, Sally Arai, David Iberri, Michaela Liedtke, David B. Miklos, Michael S. Khodadoust, Surbhi Sidana, David M. Kurtz. Tumor and immune determinants of response to anti-BCMA CAR T-cell therapy in multiple myeloma using cell-free DNA. [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 5707.