Kyoto University research group discovers effective biomarkers for CAR-T cell therapy

Chimeric antigen receptor T-cell therapy (CAR-T cell therapy) has shown particularly high efficacy in hematological cancers such as leukemia, malignant lymphoma, and multiple myeloma, and various research and development initiatives are being conducted toward clinical application in solid tumors as well. However, while some patients with hematological cancers achieve remission, cases of relapse are not uncommon.

A research group led by Professor Junko Takita, Lecturer Hidefumi Hiramatsu (currently Lecturer, Department of Pediatrics, Kindai University Faculty of Medicine), Lecturer Itaru Kato, and Project Researcher Takashi Mikami (currently Program-Specific Assistant Professor, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University) from the Department of Pediatrics, Graduate School of Medicine, Professor Akifumi Takaori-Kondo from the Department of Hematology, Graduate School of Medicine at Kyoto University, and Professor James Badger Wing from the Division of Microbiology and Immunology, Center for Infectious Disease Education and Research at the University of Osaka has revealed that when cell products contain a high proportion of specific cells in CD19 CAR-T cell therapy for relapsed or refractory B-cell precursor acute lymphoblastic leukemia (BCP-ALL), the treatment efficacy is high. These CAR-T cells produce less adenosine, which acts as an immunosuppressive, and have the properties of long-lived memory T cells, and are therefore believed to be able to effectively eliminate cancer cells. The findings were published in Cell Reports Medicine.

The research group focused on identifying differences between patients who respond well to CD19 CAR-T cell therapy and those who do not, conducting a search for biomarkers to predict treatment efficacy. CAR-T cell products as well as blood and bone marrow samples were collected from BCP-ALL patients (16 children and 3 young adults) who received treatment at Kyoto University Hospital between 2019 and 2023 over time before and after treatment and analyzed. The analysis was conducted using a combination of mass cytometry (CyTOF), droplet digital PCR, gene expression analysis, and cell assays, providing a multifaceted evaluation of CAR-T cells.

Analysis of cell markers using CyTOF revealed that when CAR-T cell products contain a high proportion of T cells characterized as CD38-negative, CD73-negative, Tim-3-negative, and HLA-DR-positive (4 marker defined: 4MD), treatment efficacy is high and relapse is less likely to occur. Among the 4MD markers, CD38 and CD73 are involved in the production of extracellular adenosine, and adenosine is known to have immunosuppressive effects. In fact, T cell assays confirmed that 4MD CAR-T cells produce less adenosine. Furthermore, gene expression analysis revealed that 4MD CAR-T cells have high oxidative phosphorylation and mitochondrial activity, possess characteristics of memory T cells, and tend to maintain immune activity over the long term. These characteristics of 4MD CAR-T cells are believed to enable them to effectively eliminate leukemia cancer cells, leading to improved recovery rates.

These results were also validated using single-cell RNA-seq data from a previous study, confirming that when patients are divided into two groups based on 4MD marker characteristics, patients who received CAR-T cell products with a high proportion of 4MD markers had fewer relapses.

The 4MD markers are related to properties such as immunological activation and exhaustion of T cells and may similarly apply to CAR-T cells for other antigens and cancers. In the future, the researchers aim to investigate whether T cells collected from patients have inherent properties that could enable efficient production of such CAR-T cells, and to develop more effective CAR-T cell therapy by examining gene transfer and culture conditions.

Mikami commented: "We will continue to strive toward new therapeutic innovations from the perspective of cancer immunology so that CAR-T cell therapy will become a source of hope for as many patients as possible."

Journal Information
Publication: Cell Reports Medicine
Title: CAR-T cells with the CD38⁻CD73⁻Tim-3⁻HLA-DR⁺ phenotype predict the efficacy of tisagenlecleucel as a treatment for B cell precursor ALL
DOI: 10.1016/j.xcrm.2025.102576