Blasts Monocytic Myeloid-Derived Suppressor Cell Skewing Is a Potential Mechanism of AML Immune-Escape

TCR-T cell therapy using T cells engineered to express high-affinity receptors targeting Wilms Tumor Antigen1 (WT1), known as T_TCR-C4, has shown promising results in the treatment of AML (Chapuis A et al., Nat Med 2019). However, immune-escape of tumor cells remains one of the biggest obstacles to successful cell therapy.

We previously described, a mechanism of immune escape characterized by a change in the proteosomal machinery compromising antigen presentation (Lahman M et al., Sci Transl Med 2022). Here, we used single-cell RNA sequencing to study a patient exhibiting long-term (> 100 days post-infusion) T_TCR-C4 persistence who experienced relapse post-infusion. Leveraging the sex mismatch between the male donor and female recipient, we tracked the transcriptome of blasts before infusion and at relapse. Specifically, we used the female-specific gene XIST and the male-specific gene RPS4Y1 and employed the marker-based purification algorithm scGate (Andreatta M et al., Bioinformatics 2022) to precisely identify the blasts. Furthermore, we identified healthy myeloid cells, endogenous CD8⁺ T cells, and T_TCR-C4 cells.

In line with clinical reports, blasts were detected before T_TCR-C4 infusion and at day 178 post-infusion. Notably, the number of T_TCR-C4 progressively declined from day 21 to day 178. Further analysis of T_TCR-C4 transcriptional changes revealed the expression of genes associated with mitochondrial fitness and energy production at day 178, suggesting activation of the mitochondrial machinery in response to the presence of blasts. T_TCR-C4 cell gene-set variation analysis showed persistence of immune-response (interferon-gamma response) and mitochondrial activity (oxidative phosphorylation) but also revealed enriched signatures of apoptosis, hypoxia, and inflammation at day 178. These findings suggested that although T_TCR-C4 could mount an immune response against the blasts, a potential change in leukemia hampered their response and induced T_TCR-C4 apoptosis and decline.

Further examination of the blasts' transcriptomes before infusion and at day 178 showed that blasts skewed towards a monocytic phenotype, expressing markers such as CD14, CCR2, and ITGAM. Prior studies (Van Galen et al., Cell 2019) have indicated that AML monocytic myeloid-derived suppressor cell (MDSC) skewing can impair T-cell responses and promote leukemic cell survival. Our analysis revealed higher expression of most MDSC genes at day 178 compared to the pre-infusion timepoint, indicating a skewing of blasts towards an MDSC phenotype. To further support these findings, we analyzed an independent bulk-RNAseq dataset from diagnostic samples of the BeatAML2 cohort (Bottomly et al., Cancer Cell 2022). Using a manually curated gene signature of monocytic MDSCs, we employed a Cox's proportional hazard model with lasso penalty to select informative genes. The resulting gene signature score, consisting of nine genes involved in mechanisms of immunosuppression and tumor survival, predicted overall survival, consistent with previous data indicating that MDSC genes adversely affect overall survival in AML patients.

Finally, we explored in-vitro strategies to control this mechanism of escape using a TCR with higher affinity for WT1 compared to T_TCR-C4, and using engineered CD4 and CD8 against the same target (WT1).

In conclusion, this case report highlights the skewing of AML blasts towards a monocytic myeloid-derived suppressor cell phenotype as a potential mechanism of immune escape. The findings underscore the need for more potent cell therapies able to prevent immune-escape and address blast heterogeneity.

Greenberg:Immunoscape: Consultancy, Current equity holder in private company; Elpiscience Biopharmaceuticals: Consultancy, Current equity holder in private company; Fibrogen: Consultancy, Current equity holder in publicly-traded company; Earli: Consultancy, Current equity holder in private company; Nextech: Consultancy, Current equity holder in private company; Rapt Therapeutics: Consultancy, Current equity holder in publicly-traded company; Affini-T Therapeutics: Consultancy, Current equity holder in private company; Catalio: Consultancy, Current equity holder in private company.