Longitudinal Profiling of the T Cell Compartment in Patients with Chronic Lymphocytic Leukemia Treated with Venetoclax

Abstract

Venetoclax (ven), an inhibitor of the BCL2 anti-apoptotic protein, has been proven remarkably effective in the treatment of patients with chronic lymphocytic leukemia (CLL), where the malignant B cells typically overexpress BCL2. BCL2 is also expressed by various bystander cells in the CLL microenvironment, including T cells. Hence, investigating the effects of ven treatment on T cells is highly relevant, especially considering that distinct T cell subpopulations exhibit different sensitivity to anti-apoptotic signaling blockade. Herein we interrogated the molecular and phenotypic profiles of the T cell compartment in 1 treatment-naïve and 15 relapsed/refractory CLL patients who received ven either as monotherapy (n=12) or in combination with an anti-CD20 antibody (obinutuzumab, n=1; rituximab, n=3). We studied peripheral blood samples collected prior to ven initiation and after 5 months of treatment, from which we isolated T cell subpopulations (CD3+ T cells n=8; CD4+ and CD8+ T cells, n=8). Longitudinal analysis of pre/post-treatment samples by flow cytometry (n=7) revealed a significant (p=0.01) decrease in the numbers of central memory (CD45RO+/CCR7+) CD4+ (21.8% vs 8.8%) and CD8+ cells (21.4% vs 9.7%) under ven; in contrast, a significant (p=0.01) increase of CD8+ effector memory cells (CD45RO+/CCR7-) was observed (27.8% vs 32.9%). Profiling of the T cell receptor beta (TRB) chain gene repertoire overtime (n=15) was performed by next generation sequencing (NGS). Clonotypes (i.e. TRBV-TRBD-TRBJ gene rearrangements with unique pairs of TRBV genes and identical CDR3 amino acid sequences) were calculated and clonality was estimated as the average cumulative frequency of the 10 most frequent clonotypes per sample (ACF-10). A significantly (p=0.01) more diverse repertoire was identified in CD4+ vs CD8+ cells at both pre- and post-treatment timepoints (average numbers of clonotypes pre-/post-treatment: CD4+ cells, 16,908/13,768; CD8+ cells, 4,437/3,633). Expanded clonotypes corresponding to oligoclonal expansions were documented in all examined subpopulations at both timepoints. However, significantly (p=0.01) more pronounced skewing was observed in CD8+ vs CD4+ cells (pre-/post-treatment ACF-10 values: 64.4%/70.6% vs 31.4%/42.2%, respectively). Repertoire comparisons overtime highlighted a fraction of T clonotypes that were retained after treatment in all examined subpopulations. Of note, repertoire conservation was significantly (p=0.01) greater in CD8+ vs CD4+ T cells [retained pre-treatment clonotypes: 7,102/31,063 (28%) vs 11,525/118,359 (12%), respectively]. Transcriptome profiling of CD4+ and CD8+ cells pre-/post-treatment was performed using the Oncomine Immune Response Research Assay (395 genes) in 5 cases attaining a complete response after treatment. While the transcriptomes of CD4+ cells remained essentially unaltered, significant differences were identified in CD8+ cells, where 19 genes were found to be downregulated (adj.p<0.05, fold change>2). These genes are implicated in functions such as immune response (e.g. TLR7, TLR9, CD40), regulation of immune system (e.g. HLA genes, CIITA, TNFAIP8) and lymphocyte activation pathways (e.g. ICOSLG, CEACAM1, CXCR5), with at least some of these having immunosuppressive functions (e.g. BTLA and CTLA4 encoding inhibitory receptors associated with T cell exhaustion). In conclusion, ven treatment led to increased numbers of CD8+ effector subpopulations along with prominent clonal expansions and transcriptional rewiring that could conceivably contribute to clinical response. Downregulation of immune-related genes implicated in core regulatory/activation pathways supports immune recovery by ven, offering a rationale for future combination strategies aiming to increase the depth of clinical response.