Upregulation of BCL11B and TCF1 in CD8+ T Cells Indicates the Reconstitution of T Cell Immunity in CLL Patients Treated with Ibrutinib
Authors: Yin Qingsong , Liang Taotao , Wang Shan , Ai Hao , Wang Qian , Wu Hongfei 
Published: December 2024

Background:
Multiple studies have demonstrated that in addition to targeted anti-tumor effects, ibrutinib can also regulate T cell immunity in patients with chronic lymphocytic leukemia (CLL). However, there are currently no definitive biomarkers to assess the rebuilding of T cell immunity in patients undergoing ibrutinib treatment. Studies have shown that the high expression of TCF1 and BCL11B correlates with T cell memory differentiation and cytotoxic functions, respectively. Moreover, our previous study showed that the high expression of TCF1 and BCL11B was associated with favorable prognoses in CLL patients.
Aims:
To investigate the changes of TCF1 and BCL11B expression in CD8+ T cells and their roles in the recovery of T cell immunity following ibrutinib treatment.
Methods:
Single-cell RNA sequencing (scRNA-seq) and ATAC data from CLL patients before and after ibrutinib treatment were retrieved from the GEO database. TCF1 and BCL11B ChIP data were obtained from the Cistrome DB Toolkit database. ScRNA-seq data, cell fate trajectories, and biological process enrichment were analyzed using R software. ATAC and ChIP data were analyzed through the UCSC Genome Browser. Peripheral blood mononuclear cells (PBMCs) from CLL patients before and after ibrutinib treatment were collected from the Affiliated Cancer Hospital of ZhengZhou University, and the expression of BCL11B and TCF1 was detected by flow cytometry.
Results:
We analyzed the changes of T cell subsets in patients who achieved good responses to ibrutinib before, and at 1, 4 and 9 months after treatment, and found that effector memory T cells (Tem) that increased before treatment gradually differentiated into effector T cells (Teff) after 4 months of ibrutinib treatment according to cell trajectory analysis. During this period, there was a transient increase in exhausted T cells (Tex) 1 month post-treatment. Concurrently, compared with pre-treatment, the proportion of Teff increased significantly in CD8+ T cells after 4-9 months of ibrutinib treatment. Moreover, the co-expression of BCL11B and TCF1 was gradually up-regulated in Teff. Subsequently, we measured the expression of BCL11B and TCF1 at different time points during ibrutinib treatment by flow cytometry and found that the percentage of TCF1+BCL11B+ T cells increased significantly in CD8+ T cells after ibrutinib treatment, especially in Teff (CD45RO+CD62L-) and Tem (CD45RO+CD62Llow) subgroups (All P values &lt; 0.0001). The proportion of TCF7+BCL11B+ cells in Tex (PD1+TIM3+) was significantly lower than that in non-Tex (PD1-TIM3-) (P value &lt; 0.0001). These findings were consistent with the scRNA-seq analysis results. To further explore the mechanisms of ibrutinib's immunomodulatory role on T cell immunity, enrichment analysis showed that the biological processes of differentially expressed genes in scRNA-seq of T cells focused on DNA methylation, involving two methylases, EZH2 and DNMT1. Further analysis of ATAC-seq data showed that during ibrutinib treatment, the chromatin accessibility of TCF1 and BCL11B significantly increased, on the contrary, the chromatin accessibility of EZH2 and DNMT1 decreased. ChIP-seq data revealed that BCL11B and TCF1 interacted, and synergistically regulated the chromatin accessibility of EZH2 and DNMT1, further inhibiting their expression.
Conclusion:
The upregulation of BCL11B and TCF1 in CD8+ T cells suggests a favorable response to ibrutinib in CLL patients, which may be attributed to ibrutinib's promotion of epigenetic regulation, leading to a decrease in Tex, thereby facilitating Tem differentiation into Teff and remodeling T cell immunity. This study provides new insights into the combination of ibrutinib with epigenetic regulatory drugs, such as EZH2 inhibitor, ultimately enhancing the efficacy of ibrutinib.
Keywords: Ibrutinib, Chronic lymphocytic leukemia, TCF1, BCL11B, epigenetic regulation, CD8+ T cell