Case Study: Hematopoietic Stem Cells in CD19 CAR T-cell Therapy Resistance Study

Acute lymphoblastic leukemia (ALL) stands as the most prevalent childhood cancer, with relapsed cases historically posing significant challenges to treatment. Despite impressive survival rates for newly diagnosed patients, those facing relapse encounter daunting odds, with survival rates plummeting below 30%. A beacon of hope in this landscape is CD19 CAR T-cell therapy (CART19), boasting remarkable response rates ranging from 80% to 90% in relapsed/refractory disease. However, a pressing conundrum persists: the enigmatic nature of antigen-independent factors that confer resistance to CART19 remains poorly understood. In this pursuit, scientists embarked on a groundbreaking study to decipher the distinct characteristics of resistant leukemias, seeking to unveil predictive markers before therapy initiation.

Methods:In a clinical trial conducted at Seattle Children’s Hospital (PLAT-02), researchers procured pre-treatment bone marrow aspirates (BMAs) from enrolled patients to scrutinize disparities between resistant and sensitive leukemias. Patient responses were categorized, with non-response defined as the failure to achieve and sustain minimal residual disease negativity at Day +63. The study cohort comprised 7 resistant and 7 sensitive leukemias as controls. Employing a comprehensive array of analytical techniques, including whole exome sequencing, bulk RNA-seq, PacBio-seq of the CD19 locus, array-based methylation, ATAC-seq, single-cell RNA-seq (scRNA-seq), and CyTOF, researchers delved into the molecular intricacies underlying treatment resistance.

Results:The pivotal role of hematopoietic stem cells (HSCs) emerged prominently through the ATAC-seq analysis. Gene set enrichment analysis of ATAC-seq data unveiled heightened chromatin accessibility at regions associated with stem cell proliferation (NES = 2.31; p < 0.0001) and cell cycling (NES = 2.27; p < 0.0001) in resistant leukemias. Notably, a striking resemblance was observed between the accessibility patterns of non-responders and hematopoietic progenitors, including HSCs (p = 0.037) and common myeloid progenitors (p = 0.047). This finding was further substantiated by an elevated frequency of cell subpopulations expressing a multi-lineage phenotype (CD19, CD20, CD33, CD34; p = 0.009). Additionally, a significant downregulation of antigen presentation and processing pathways across all leukemic cells relative to responders was noted (p = 0.0001).

Conclusions:The ATAC-seq analysis sheds invaluable light on the pivotal role of hematopoietic stem cells in predicting the efficacy of CAR T-cell therapy. These findings underscore the imperative for refining eligibility criteria for CART19 in pediatric leukemia patients and highlight the urgency of exploring alternative or complementary therapeutic avenues for those deemed resistant. As research progresses, harnessing these insights holds immense potential to revolutionize treatment paradigms and enhance outcomes for children battling this formidable hematological condition.

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Source: https://aacrjournals.org/cancerres/article/82/12_Supplement/3581/702336