Single-Cell Sequencing Analysis Reveals Cellular Dynamics Underlying Different Responses to Blinatumomab in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia
Authors: Zhang Mingying , Zhang Yuanyuan , Qi Peijing , Lin Wei , Wu Ying , Yu Jiaole , Zheng Huyong , Zhang Ruidong 
Published: December 2024

Introduction: Blinatumomab, a bispecific antibody that directs CD3 T cells to CD19 leukemic cells, shows promise in treating pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Samples for this study were obtained from children enrolled in an open-label, single-arm clinical trial (ChiCTR2400083570) that advances blinatumomab to the induction chemotherapy stage. Despite its potential, not all patients respond well to this treatment, making it crucial to elucidate the specific mechanisms underlying the varied responses to blinatumomab in BCP-ALL.
Methods: Seven pediatric BCP-ALL patients with positive minimal residual disease (MRD, ≥1%) after 15 days of routine induction chemotherapy were included in our study and subsequently received a 28-day blinatumomab treatment. Bulk RNA-sequencing (RNA-seq) was used to determine the baseline cellular abundance of BCP-ALL. Single-cell RNA-sequencing (scRNA-seq) was performed to characterize the cellular dynamics of the B and T cells, as well as the B-cell and T-cell receptor (BCR/TCR) repertoires in BCP-ALL patients before, and on day 14 and 28 during blinatumomab treatment.
Results: Among 7 patients, 2 patients (P-1 and P-2) remained MRD+ at all surveillance time points (insensitive group), while the other 5 patients achieved MRD- (MFC MRD&lt;10-4 or NGS MRD&lt;10-6) on day 14 (P-3) or day 28 (P-4, P-5, P-6 and P-7) following blinatumomab treatment (sensitive group). Using a Bayesian method with scRNA-seq as prior information, we predicted the cellular composition of B-ALL from bulk RNA-seq data. Our findings indicated that the insensitive group had higher levels of hematopoietic stem cells (HSC) and common lymphoid precursors (CLP) compared to the sensitive group. This suggests that elevated proportions of HSC and CLP are strongly associated with a reduced response to blinatumomab.
Pseudo-time analysis revealed that B cells in the sensitive group followed a normal developmental trajectory, where HSC differentiated into pro-B, pre-B, immature B, or plasma cells. In contrast, B cells in the insensitive group displayed an abnormal trajectory, with differentiation predominantly reverting from plasma or immature B cells back to HSC. Similarly, T-cell subsets exhibited comparable differences in developmental trajectories between the sensitive and insensitive groups.
During 28-day blinatumomab treatment, the percentage of effector T cells (Teff) in the sensitive group initially decreased but then increased, while in the insensitive group, the percentage of Teff continuously declined. Both groups showed a rise and subsequent fall in the proportion of exhausted T cells (Tex). Notably, we identified two distinct Tex clusters: CXCR6-Tex and MKI67-Tex. On day 14, the abundance of CXCR6-Tex and MKI67-Tex was significantly higher in the sensitive group compared to the insensitive group. Shared TCR clones and similar core transcription factors (TFs) expression patterns between the Teff and CXCR6-Tex, as well as CXCR6-Tex and MKI67-Tex, support the presence of a differentiation trajectory. We hypothesize that blinatumomab treatment may cause some Teff to first convert to CXCR6-Tex, with a subset then further converting to MKI67-Tex. Interestingly, MKI67-Tex exhibited high expression of genes related to the TCR signaling pathway and cytotoxic effector molecules, including granzymes B, A, and K, suggesting that MKI67-Tex may play a role in killing leukemic cells.
Conclusion: This study illuminates cellular dynamics during blinatumomab treatment and provides new insights into its mechanism of action in BCP-ALL. Detailly, on day 14, leukemic cells are still present in the majority of patients (6/7, 85.7%), indicating that extending blinatumomab treatment to 28 days is necessary for BCP-ALL patients who do not achieve MRD- after 15 days of routine induction chemotherapy. Blinatumomab prompts Teff cells to target leukemic cells, leading to the conversion of some Teff to Tex. Notably, MKI67-Tex, identified in our study, also exhibits anti-tumor effects. Additionally, insensitive group shows higher levels of stem cell infiltration and abnormal differentiation trajectories, which may be a potential mechanism of resistance to blinatumomab.