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558 Single cell RNA and TCR sequencing reveal candidate immune biomarkers of NKX019 clinical response in non-Hodgkin lymphoma (NHL)

jitc · 2025-11-04 · canonical JSON source

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Background NKX019 is a cryopreserved, allogeneic CD19-targeting chimeric antigen receptor (CAR) natural killer (NK) cell therapy engineered with membrane-bound IL-15 for enhanced persistence and cytotoxicity. Preclinical data have demonstrated potent anti-tumor activity 1 and results from a Phase I clinical trial (NCT05020678) indicated a favorable safety profile and promising efficacy across multiple non-Hodgkin lymphoma (NHL) subtypes. At the highest NKX019 dose levels, 80% of NHL patients responded to treatment, with 70% achieving complete responses.2 To elucidate mechanisms underlying therapeutic response and resistance, we conducted an exploratory single-cell transcriptomic analysis to identify baseline immune biomarkers predictive of NKX019 clinical efficacy. Given the adaptive nature of anti-cancer immune responses,3 we hypothesized that differences in antigen-presenting cell (APC) abundance, human leukocyte antigen (HLA) gene expression, and T cell receptor (TCR) repertoire diversity might correlate with response outcomes.Methods Peripheral blood mononuclear cells (PBMCs) were collected from NHL patients prior to NKX019 infusion. Single cell transcriptome and paired TCR sequencing were performed using the 10x Genomics 5’ Single Cell Gene Expression platform.Results At baseline, responders exhibited a significant enrichment of monocytes with elevated expression of HLA class I and II gene module scores. Pathway enrichment analysis revealed upregulation of antigen presentation, lymphocyte activation, cell-cell adhesion, and T cell-mediated immune pathways. In addition, CD8 + T cells from responders demonstrated increased expression of stem-like transcriptional signatures and broader TCR clonotype diversity at baseline compared to non-responders.Ligand-receptor interaction analysis4 revealed a greater number of differential interactions involving HLA genes on monocytes and their corresponding receptors on CD4+ T cells, CD8+ T cells, and NK cells in responders, suggesting a potential mechanism in which monocyte-driven adaptive T cell immune responses contribute to deepening clinical responses to NKX019.Conversely, non-responders exhibited an enrichment of dysregulated monocytes characterized by low HLA-DR expression, consistent with a myeloid derived suppressive cell (MDSC)-like phenotype known to impair anti-tumor immunity.5 Conclusions These findings suggest that a pre-existing, immunocompetent peripheral immune landscape characterized by activated monocytes and diverse, stem-like T cells may predict favorable clinical responses to NKX019 in NHL patients. In contrast, expansion of dysregulated, suppressive monocyte populations may underlie NKX019 treatment resistance. Our results support further investigation into immune-based patient stratification strategies and therapeutic combinations aimed at overcoming resistance mechanisms. These findings may also provide a rationale for investigating NKX019 in earlier lines of therapy in patients with preserved adaptive immunity.Trial Registration NCT05020678References Morisot N, Wadsworth S, Davis T, et al. 127 Preclinical evaluation of NKX019, a CD19-targeting CAR NK cell. J ImmunoTherapy Cancer 2020;8(suppl 3):A78.Dickinson M, et al. First in human data of NKX019, an allogeneic CAR NK for the treatment of relapsed/refractory (r/r) B-cell malignancies. EHA. 2023;S261.Daniel S Shen, Ira Mellman. Oncology meets immunology: the cancer-immunity cycle. Immunity. 2013. doi.org/10.1016/j.immuni.2013.07.012Browaeys R, et al. MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data. bioRxiv 2023. doi:10.1101/2023.06.13.544751.Bourbon E, et al. HLA-DR expression on monocytes and outcome of anti-CD19 CAR T-cell therapy for large B-cell lymphoma. Blood Advances. 2023;7:744–755.Ethics Approval This Phase 1, multicenter, open-label study (NKX019-101; ClinicalTrials.gov Identifier: NCT05020678) was reviewed and approved by the relevant institutional review board(s) and/or ethics committee(s) at each participating site. All procedures involving human participants complied with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. Written informed consent was obtained from all individual participants before enrollment in the study