Single-cell antigen-specific landscape of CAR T infusion product identifies determinants of CD19-positive relapse in patients with ALL

Abstract

A notable number of acute lymphoblastic leukemia (ALL) patients develop CD19-positive relapse within 1 year after receiving chimeric antigen receptor (CAR) T cell therapy. It remains unclear if the long-term response is associated with the characteristics of CAR T cells in infusion products, hindering the identification of biomarkers to predict therapeutic outcomes. Here, we present 101,326 single-cell transcriptomes and surface protein landscape from the infusion products of 12 ALL patients. We observed substantial heterogeneity in the antigen-specific activation states, among which a deficiency of T helper 2 function was associated with CD19-positive relapse compared with durable responders (remission, >54 months). Proteomic data revealed that the frequency of early memory T cells, rather than activation or coinhibitory signatures, could distinguish the relapse. These findings were corroborated by independent functional profiling of 49 patients, and an integrative model was developed to predict the response. Our data unveil the molecular mechanisms that may inform strategies to boost specific T cell function to maintain long-term remission.

T-cell potential for CD19-expressing malignancies revealed by multi-dimensional single-cell profiling

“…While signatures of CD8 T cells are associated with immediate antitumor function including cytotoxicity, CD4 T cells signatures are primed for long-term persistence. Collectively, these data present a testable hypothesis of division of labor between the T cell subsets, and are consistent with emerging data for the role of CD4 CAR T cells in long term durable responses 21,45 .…”

Transcriptional states of CAR-T infusion relate to neurotoxicity – lessons from high-resolution single-cell SOM expression portraying

“…Importantly, the expression landscape established here will be used as a reference system to map independent data, for example to investigate expression patterns in published single-cell RNAseq data [e.g. derived from ( 13 ) or ( 50 )], to disentangle cellular identities and transcriptional states of bulk samples, and to extend the analyses presented here by future studies in terms of additional patient samples and longitudinal measurements. scSOM provides two different approaches for this: Firstly, novel data can be projected into the map, providing expression portraits, module expression patterns, and PAT assignments for direct comparison with the results discussed here.…”

Potential solutions for manufacture of CAR T cells in cancer immunotherapy

“…Strong efforts by both the pharmaceutical industry and academic institutions have significantly shortened the manufacturing time from approximately 14 days down to a few days or, even, 1 day 5 . Because the patient's individual leukapheresis cells and subsequent CAR T cell subpopulations influence clinical success [6][7][8][9][10] , manufacturing protocols and cytokine cocktails could be refined to enrich or select favorable and non-exhausted T cell subpopulations. In the future, further biological research, process development and hardware technologies will optimize the manufacturing of autologous CAR T cells, but throughput limitations will remain with regard to the personalized, that is individualized, setting.…”