Prior Chemotherapy Deteriorates T Cell Quality for CAR T Cell Therapy in B-Cell Non-Hodgkin’s Lymphoma

Chimeric antigen receptor (CAR) T cell therapy depends on T cells that are genetically modified to recognize and attack cancer cells. Their effectiveness thus hinges on the functionality of a patient’s own T cells. However, CAR T cell therapy is currently only approved for advanced cancers after at least one line of chemotherapy. To evaluate the potential negative effects of prior exposure to chemotherapy on T cell functionality we studied T cells of two B cell Non-Hodgkin’s lymphoma (B-NHL) patient cohorts, one collected before treatment (pre-therapy) and the other after one or more (median 3) lines of chemotherapy (post-therapy). Leveraging advanced multi-parameter flow cytometry and single-cell RNA sequencing (scRNAseq), we elucidated significant modifications in T cell subsets and their transcriptional profiles post-therapy. Our analysis revealed a discernible shift towards phenotypically more differentiated T cells and an upregulation of markers indicative of T cell exhaustion. Additionally, scRNAseq and DNA methylation analyses revealed gene expression and epigenetic changes associated with diminished functionality in post-therapy T cells. Cytotoxicity assays demonstrated superior killing efficacy of CAR T cells derived from treatment-naïve patients compared to those with chemotherapy history. These findings corroborate that employing T cells collected prior to frontline chemotherapy could enhance the effectiveness of CAR T cell therapy and improve patient outcomes. We sequenced T cells of a total of 12 B-NHL patients, six of whom did not yet receive any anti-lymphoma treatment (pre-therapy), while the other six received at least one line of therapy (post-therapy). Peripheral blood samples were collected from the above-mentioned patients and T cells were isolated. *************************************************************** Raw data unavailable due to patient privacy restrictions. ***************************************************************