Mass Cytometry Reveals PD1 Upregulation Is an Early Step in MDS Disease Progression
Authors: Coats Thomas , Smith Alexander e , Mourikis Thanos P , Irish Jonathan Michael , Kordasti Shahram , Mufti Ghulam J 
Published: October 2019

Abstract
Background
MDS is characterized by ineffective haematopoiesis and a propensity to leukaemia transformation, with increasing evidence linking immune exhaustion to disease progression. Immune checkpoints are known to be upregulated on T cells in cancer, and inhibitors of CTLA-4 and PD1/PLD1 axis have demonstrated efficacy with likely clinical benefit in MDS. We have previously shown profound changes in both the number and function of components of the adaptive immune system, particularly Tregs, in MDS (Kordasti, Blood 2007). In order to characterise the immune signature in a wider range of T cell subsets simultaneously, with particular emphasis on cells likely to be affected by checkpoint inhibitor therapy (CPI), we analyse CTLA-4 and PD1 expression in MDS by cytometry by time-of-flight (CyTOF). Additionally, we aim to explore whether these differences are accentuated by the absence or presence of somatic mutations, or in morphologically more advanced disease.
Materials and Methods
MDS patients (n=56) and age-matched healthy donors (HD, n=6) were stained with two panels of 35 and 34 antibodies for unstimulated and PMA/Ionomycin-stimulated PBMCs, respectively. Samples were run on CyTOF and data analysed using visual stochastic neighbour embedding (viSNE, Cytobank) to generate t-distributed SNE scores by unsupervised multi-dimensional reduction of T cells. Spanning-tree progression analysis of density-normalized events (SPADE), was performed and T cell subsets identified from heat maps based on typical phenotypic markers (Regulatory, Naive, Memory, Effector Memory (EM) Central Memory (CM), Effector, Terminal Effector (TE)). T cells were also clustered based on cytokine secretion (IFN-ϒ, TNF-α, IL-17, IL-2 and IL-10).
Somatic mutation analysis was performed on 48 of the MDS patients using our established targeted panel of 24 genes known to be mutated in MDS, for subgroup analysis (Mohamedali, Leukaemia 2015)
Results and Discussion
Demographics and subgroups are outlined in figure 1.
The number of Tregs was significantly higher in RAEB than non-RAEB MDS (9.6% of total CD4+ cells vs 7.5% p=0.02) and in RAEB versus HD (9.6% vs 5.8% p=0.01). There was a significantly higher proportion of Tregs in MDS patients with somatic mutations compared to those without (8.7% vs 7.06% p<0.05) and HD (8.7% vs 5.9% p<0.05), confirming our previous findings. Amongst two subpopulations of Tregs previously identified (Kordasti, Blood 2016) there was no difference between HD and MDS in terms of their number. However, Tregs A and B have an increased PD1 expression in MDS vs HD (p=0.03 & p=0.003). In addition, CD4+EM and CD4+Memory, CD4+/CD8+ Na•ve T cells and TNF-α secreting cells all expressed more PD1 when compared to HD (p<0.05), see figure 2. However, there were no differences in T cell PD1 expression when comparing low and high risk MDS patients, suggesting immune exhaustion to tumour antigens is a common founder event in MDS.
By contrast, CTLA-4 expression was not significantly different in T cell subsets between MDS and HD. Sub-groups based on specific somatic mutations did reveal that CD4+ Memory, CD4+TE and CD8+CM subsets in SF3B1-mutated MDS cases had less CTLA-4 expression compared to MDS cases with other mutations (p<0.05). Furthermore, SF3B1-mutant cases also had less CTLA-4 expression when compared to MDS cases without any detected mutations in CD4+ Memory, CD4+EM and CD8+CM subsets (p<0.05).
Taken together this work suggests a possible 3 hit-model for disease progression in MDS. The establishment of MDS is accompanied by increased expression of PD1 most likely in response to increased PDL1 on tumour cells, which argues for early introduction of PD1 inhibitor in the disease course. Increased CTLA-4 expression is likely a later step, dependent on the acquisition of specific mutations by the malignant clone, that further alters the relationship between tumour and immune surveillance. Finally, in disease progression through from non-RAEB to RAEB/AML there is an expansion of suppressive Tregs facilitating tumour outgrowth. Furthermore, pro-inflammatory IL17 secreting T helper cells (Th17) have been shown to be increased in low risk MDS and are known to be associated with autoimmune disease. The trend towards increased PD1 expression in Th17 cells in a group of low risk patients harbouring SF3B1 mutations (p=0.09) is suggestive that acquisition of increased PD1 expression is a key branch point in disease outcome.

Disclosures
Irish: Incyte: Research Funding; Janssen: Research Funding; Cytobank, Inc.: Equity Ownership, Membership on an entity's Board of Directors or advisory committees.