Deciphering the Landscape of Peripheral Blood T Cells via Single-Cell RNA-Seq in Chronic Lymphocytic Leukemia

Background: Chronic Lymphocytic Leukemia (CLL) is a deliberating lymphoproliferative disease characterized by profound immune deficiencies mediated by abnormal peripheral blood T cells, however, the immune landscape of T cells in CLL patients remains poorly understood, especially at the single cell level. Methods: We performed single-cell RNA sequencing on peripheral blood T cells from 3 CLL patients and 4 healthy donors. Dimension reduction and pseudotime analysis were applied to identify T cell subsets, their fraction changes and developmental trajectory in CLL. We also examined the association of T-cell subsets with prognosis using peripheral blood transcriptome data of CLL patients. Findings: We identified 10 T-cell subsets from single-cell RNA-seq of more than 20,000 T cells. Both CD4+ and CD8+ naive T cells were greatly reduced in CLL patients compared to healthy donors, and reduced expression of naive T cell markers in peripheral blood predicted a worse prognosis of CLL patients. We also revealed that a specific T cell state with high expression of GZMK, CD69, and AP-1, which are associated with T cell deficiency in CLL. Interpretation: Our results demonstrated that systematic rewiring of peripheral blood T-cell subsets fraction and their molecular signatures in CLL. The immune deficiency of CLL was driven by altered developmental trajectories of T cells with abnormal expression of GZMK, CD69 and AP-1. Funding Statement: The research was supported by the grants from CAMS Innovation Fund for Medical Sciences (CIFMS 2017-I2M-1–015; 2017-I2M-3-018; 2018-I2M-AI-010), National Natural Science Foundation of China (81600181, and 81701840), Natural Science Foundation of Tianjin City (18JCQNJC12100), and Tianjin Second Batch of Special Support Plan for Talent Development High Level Innovation and Entrepreneurship Team (TJTZJH-GCCCXCYTD-2-18). Declaration of Interests: The authors declare no competing financial interests. Ethics Approval Statement: This study was approved by the Ethics Committee of the Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences. All participating subjects have signed the informed consent