Liquid biopsy approach to monitor the efficacy and response to CAR-T cell therapy

Stephanie N Shishido; Olivia Hart; Sujin Jeong; Aidan Moriarty; Darren Heeke; John Rossi; Adrian Bot; Peter Kuhn

doi:10.1136/jitc-2023-007329

Liquid biopsy approach to monitor the efficacy and response to CAR-T cell therapy

J Immunother Cancer. 2024 Feb 12;12(2):e007329. doi: 10.1136/jitc-2023-007329.

Authors

Stephanie N Shishido¹, Olivia Hart¹, Sujin Jeong¹, Aidan Moriarty¹, Darren Heeke², John Rossi², Adrian Bot², Peter Kuhn^{3

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Affiliations

¹ Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California, USA.
² Kite A Gilead Company, Santa Monica, California, USA.
³ Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California, USA [email protected].
⁴ Department of Biological Sciences Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California, USA.
⁵ Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA.
⁶ Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA.
⁷ Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
⁸ Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.

Abstract

Background: Chimeric antigen receptor (CAR)-T cells are approved for use in the treatment of hematological malignancies. Axicabtagene ciloleucel (YESCARTA) and brexucabtagene autoleucel (TECARTUS) genetically modified autologous T cells expressing an anti-CD19 scFv based on the FMC63 clone have shown impressive response rates for the treatment of CD19+B cell malignancies, but there remain challenges in monitoring long-term persistence as well as the functional characterization of low-level persisting CAR-T cells in patients. Furthermore, due to CD19-negative driven relapse, having the capability to monitor patients with simultaneous detection of the B cell malignancy and persisting CAR-T cells in patient peripheral blood is important for ensuring timely treatment optionality and understanding relapse.

Methods: This study demonstrates the development and technical validation of a comprehensive liquid biopsy, high-definition single cell assay (HDSCA)-HemeCAR for (1) KTE-X19 CAR-T cell identification and analysis and (2) simultaneously monitoring the CD19-epitope landscape on neoplastic B cells in cryopreserved or fresh peripheral blood. Proprietary anti-CD19 CAR reagents, healthy donor transduced CAR-T cells, and patient samples consisting of malignant B cell fractions from manufacturing were used for assay development.

Results: The CAR-T assay showed an approximate limit of detection at 1 cell in 3 million with a sensitivity of 91%. Genomic analysis was additionally used to confirm the presence of the CAR transgene. This study additionally reports the successful completion of two B cell assays with multiple CD19 variants (FMC63 and LE-CD19) and a unique fourth channel biomarker (CD20 or CD22). In patient samples, we observed that CD19 isoforms were highly heterogeneous both intrapatient and interpatient.

Conclusions: With the simultaneous detection of the CAR-T cells and the B cell malignancy in patient peripheral blood, the HDSCA-HemeCAR workflow may be considered for risk monitoring and patient management.

Keywords: Hematologic Neoplasms; Immunoassay; Immunotherapy; Neoplastic Cells, Circulating; Receptors, Chimeric Antigen.

MeSH terms

Antigens, CD19
Cell- and Tissue-Based Therapy
Humans
Neoplasms*
Receptors, Antigen, T-Cell / genetics
Receptors, Chimeric Antigen* / genetics
Recurrence

Substances

Receptors, Chimeric Antigen
Receptors, Antigen, T-Cell
Antigens, CD19