Characterization of Leukemic Resistance to CD19-Targeted CAR T-cell Therapy through Deep Genomic Sequencing

Area of Science:

• Immunology
• Genetics
• Oncology

Background:

• Chimeric antigen receptor (CAR) T-cell therapy targeting CD19 is effective against pediatric B-cell acute lymphoblastic leukemia (B-ALL).
• Relapse can occur due to the loss of the CD19 target antigen on leukemia cells.
• Understanding the genetic basis of CD19 loss is crucial for improving CAR T-cell therapy efficacy.

Purpose of the Study:

• To clarify and strengthen the relationship between genomic events and CD19 loss in relapsed B-ALL after CAR T-cell therapy.
• To identify specific mutations and genetic alterations in CD19 that lead to resistance against CD19-targeted CAR T-cell therapy.

Main Methods:

• Deep whole-exome sequencing was performed on pre-treatment and relapse leukemia cells from 13 pediatric B-ALL patients treated with CAR T-cell therapy.
• Analysis focused on identifying single-nucleotide variants, small insertions/deletions (indels), and gene deletions within the CD19 gene.
• Patient-derived xenograft models were utilized to expand leukemic cells for comprehensive genomic analysis.

Main Results:

• Relapse-specific single-nucleotide variants, small indels, and CD19 gene deletions were identified in patients with CD19-negative relapse.
• These genetic alterations in CD19 were specific to the CD19-negative relapse group.
• One patient had a pre-existing CD19 deletion and genomic instability prior to therapy, suggesting an initial hit for subsequent CD19-negative relapse.
• Pre-existing mutations and genomic instability were not significant predictors of CD19-negative relapse across all patients, possibly due to sample size limitations.

Conclusions:

• Genomic events, including specific mutations and deletions in the CD19 gene, are strongly associated with CD19-negative relapse in pediatric B-ALL patients treated with CAR T-cell therapy.
• These findings elucidate a critical mechanism of resistance to CD19-targeted immunotherapy.
• Further research is needed to explore the role of pre-existing mutations and genomic instability in predicting relapse, considering potential limitations in sample size.