A Single-Cell T-Cell Reference Map Delineates the Biological Landscape of CD4+ T Cells in Myelodysplastic Syndromes Under Venetoclax Therapy

Understanding the dynamic changes in T-cell subtypes during therapy is essential for developing effective therapeutic combinations to improve clinical outcomes. To assess whether the immune system contributes to the therapeutic effect of venetoclax, the most promising agent for patients with higher-risk myelodysplastic syndromes (MDS) that progress after hypomethylating agent (HMA) failure, we performed cytometry by time-of-flight analysis (with a panel of 59 antibodies) of sequential bone marrow (BM) samples from MDS patients enrolled in trials of venetoclax. A subset of CD4⁺ T cells expanded only in patients with marrow complete remission at venetoclax response. To validate these results, we used flow cytometry to analyze the frequencies of naïve (CD45RA⁺CD45RO^- CD95^-CCR7⁺⁺), stem cell–like memory (SCM; CD45RA⁺CD45RO^-CD95⁺CCR7⁺), central memory (CM; CD45RA^-CD45RO⁺CD95⁺CCR7⁺), effector memory (EM; CD45RA^-CD45RO⁺CD95⁺CCR7^-) and terminal effector (TE; CD45RA⁺CD45RO^-CD95⁺CCR7^-) CD8⁺ or CD4⁺ T cells and CD4⁺CD25⁺CD127^lowFOXP3⁺ T regulatory cells (Tregs) in sequential BM samples isolated from 25 patients who received venetoclax. These analyses confirmed that naïve, SCM, and EM CD4⁺ T-cells significantly expanded at response, whereas Tregs expanded at disease progression. The T-cell subsets’ dynamics were specific to venetoclax alone or in combination with HMAs, as they were not observed in patients treated with HMAs alone. No significant changes in the CD8⁺ T-cell compartment during venetoclax treatment were noted. In contrast, only a slight increase of CD8⁺ TE cells was observed (P= 0.055).

To explore the contribution of T-cell phenotypic states to venetoclax-induced responses and assess clonality and antigen recognition prediction, we performed transcriptomic and T-cell receptor (TCR) analyses using different single-cell multi-omics platforms. Single-cell proteo-genomic analyses (with a panel of 32 antibodies) of CD3⁺ cells isolated at different times during venetoclax therapy (15 samples from 5 patients; 34,229 sequenced T cells) allowed us to develop specific transcriptomic signatures for each T-cell subtype, which we applied to interrogate a larger cohort of sequential samples analyzed by scRNA- and/or scTCR-sequencing analyses (64 CD3⁺ samples from 12 patients; 124,871 sequenced T cells). This comprehensive approach confirmed the significant expansion of SCM CD4⁺ T cells at treatment response and the reduction of these cells at disease relapse, previously observed by flow cytometry analysis. SCM CD4⁺ T cells had significantly upregulated gene expression programs associated with cytokine secretion and cytotoxicity at disease response but expressed increased levels of exhaustion-related genes at disease relapse.

MDS patients whose disease responded to venetoclax-based therapy showed a higher count of CD4⁺ EM T-cell clonotypes and greater T-cell diversity at baseline, whereas a reduction in these clonotypes during therapy predicted disease progression. SCM and EM CD4⁺ T cells had the highest rates of TCR sharing, which suggests a close interplay between these subsets. Cytokine secretion assays showed that compared with naïve and CM CD4⁺ T cells, SCM CD4⁺ T cells cocultured with MDS cells secreted higher levels of IFN-γ, TNF-α, and granzyme B (GZMB), a cytokine profile resembling that of EM and TE cells. Upon tumoral challenge, venetoclax also significantly increased IFN-γ, TNF-α, and GZMB levels in SCM and EM CD4⁺ T cells.

Our study demonstrates that a subset of CD4⁺ T cells with SCM features contributes to the outcomes of MDS patients enrolled in trials of venetoclax-based therapy. SCM cells are transcriptionally and functionally similar to EM and TE cells and undergo the greatest improvement in cytotoxic capabilities and pro-inflammatory cytokine secretion upon venetoclax exposure. Thus, adoptive immunotherapy strategies have a potential role in enhancing venetoclax efficacy and preventing immune-mediated venetoclax resistance.