Abstract B047: Transcriptional signatures associated with persisting CD19 CAR-T cells in children with leukemia
Authors: Anderson Nathaniel D. , Birch Jack , Accogli Theo , Criado Ignacio , Khabirova Eleonora , Parks Conor , Wood Yvette , Young Matthew D. , Porter Tarryn , Richardson Rachel , Albon Sarah J. , Popova Bilyana , Lopes Andre , Wynn Robert , Hough Rachael , Gohil Satyen H. , Pule Martin , Amrolia Persis J. , Behjati Sam , Ghorashian Sara 
Published: September 2024

Chimeric antigen receptor (CAR)-modified T-cells have become established as an effective treatment of haematological cancers. In the context of relapsed and refractory childhood pre-B cell acute lymphoblastic leukaemia (B ALL), CD19 targeting CAR T-cells often induce durable remissions. One of the most critical determinants of achieving a durable response is the persistence of CAR T-cells. Here, we systematically analysed CD19 CAR T cells of ten children with relapsed or refractory B ALL enrolled in the CARPALL trial (NCT02443831). We performed high throughput single-cell gene expression and T-cell receptor (TCR) sequencing of infusion products and serial blood and bone marrow samples up to five years post-infusion. We first found that late, long-lived CAR T cells developed a CD4/CD8 double-negative (DN) phenotype characterised by GZMK+ exhausted-like memory state. Our key finding was that the most recurrent and strongest markers of long-lived CAR-T cells generated a persisting CAR T signature that was delineated by the expression of bona fide immune-related genes, such as TIGIT and GPR183, as well as genes with unknown or emerging roles in immune biology. This signature emerged across clonotypes and subsets of T-cells, indicating that CAR T-cells converge transcriptionally when a durable clinical response is achieved. Remarkably, we also detected this persistence signature in recipients of a different CD19 CAR T-cell product that maintained decade long remissions in two adult patients with chronic lymphocytic leukaemia. Examination of single T-cell transcriptomes from a wide range of healthy and diseased tissues across children and adults indicated that the persistence signature is rarely encountered in other settings. Accordingly, we found a persistence signature that appears to be independent of infusion product, patient age, and leukaemia type. These findings raise the possibility that a universal transcriptional signature of clinically effective, persistent CD19 CAR T cells exist. It may provide a basis for the identification of biomarkers of persistence and guide refinement of manufacturing methods.

Citation Format: Nathaniel D. Anderson, Jack Birch, Theo Accogli, Ignacio Criado, Eleonora Khabirova, Conor Parks, Yvette Wood, Matthew D. Young, Tarryn Porter, Rachel Richardson, Sarah J. Albon, Bilyana Popova, Andre Lopes, Robert Wynn, Rachael Hough, Satyen H. Gohil, Martin Pule, Persis J. Amrolia, Sam Behjati, Sara Ghorashian. Transcriptional signatures associated with persisting CD19 CAR-T cells in children with leukemia [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pediatric Cancer Research; 2024 Sep 5-8; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl):Abstract nr B047.