Loss of the Y chromosome defines a biologically distinct subtype of Acute Myeloid Leukemia (AML), associated with decreased inflammatory response patterns, and favorable outcomes in young male patients (pts)

Abstract

Abstract Loss of the Y chromosome (LOY) is often detected in AML, yet it has been mostly considered inconsequential, assuming it is associated with aging. We did an integrated clinical, transcriptomic, and immunophenotypic analysis, and found that LOY may define a biologically and clinically distinct AML subtype with direct implications in disease biology and prognosis.Male AML pts <60y with sole LOY treated with intensive chemotherapy on frontline protocols of the CALGB Alliance and Flatiron Health database had a 3-year overall survival (OS) rate of 60% (95% CI, 25-83) and 89% (95% CI, 43-98), respectively. This is comparable to the 2022 ELN favorable risk groups (63%, 58–67; n=249, and 71%, 64–77; n=240, respectively) and significantly higher than the intermediate and adverse ELN groups. In male pts <60 years with cytogenetically normal AML (CN-AML) who were treated with intensive chemotherapy on Alliance frontline protocols (n=291), lower expression of Y-linked genes, as derived from bulk RNA sequencing, was associated with 3-year disease-free survival (DFS) rate of 56% (95% CI, 38-70), which was significantly longer than DFS of male pts with high Y-linked gene expression (37%, 95% CI 32-43). These findings suggest that Y chromosome dosage and activity may influence AML clinical outcome.To understand the mechanistic basis of these observations, we performed bulk RNA sequencing in diagnostic bone marrow (BM) samples from 23 AML pts with sole LOY, 218 age-matched male and 203 female pts with CN-AML. LOY AML males showed a distinct transcriptomic profile compared to both other groups, including 364 genes (2.3%) upregulated and 74 genes (0.46%) downregulated in the LOY compared with the CN-AML male samples (Padj<0.05). Among the top upregulated genes were SOX11, SOX17, MECOM, ID4 and CDH2. Pathway analysis of the upregulated genes showed enrichment for extracellular matrix and cell adhesion modules, angiogenesis and vascular-niche factors as well as regulation of TGFβ and the canonical Wnt signaling.In contrast, the downregulated genes showed a profound enrichment in pathways related to innate immune regulation, such as inflammatory response and Toll-Like Receptor (TLR) signaling pathways. In line with this, Gene Set Enrichment Analysis showed that terms related to T cell activation, TLR signaling and NFκB activity were significantly downregulated in the LOY male samples compared with their CN-AML counterparts (Padj<0.05), indicating a broad suppression of innate and adaptive immune responses.We used high-dimensional flow cytometry to validate these transcriptional findings in 8 BM mononuclear (BMMC) samples from male AML pts with LOY as a sole cytogenetic abnormality, and 8 male CN-AML pts. While the overall frequencies of CD4⁺ and CD8⁺ T-cells were comparable between groups, the CD8⁺ compartment in LOY AML was skewed toward CD45RA-CD45RO+CD28+ memory-like phenotypes (Tm) (P=0.02), with a striking decrease of terminal effector (Teff) CD45RA+CD45RO-CD27-CD28- cells (P=0.0001), resulting in a significantly reduced Teff:Tm ratio, which was validated in a second cohort BM samples. Additional analyses revealed decreased trends in dendritic, NK, and B cells, consistent with a broadly immune-compromised marrow environment.Finally, fluorescence in situ hybridization in sorted leukemic cells and autologous T cells from 3 LOY pts showed that LOY was restricted to blasts and was absent from CD4⁺ and CD8⁺ T cells, indicating that the immune alterations possibly arise from non-cell-autonomous mechanisms driven by LOY AML cells. In line with this finding, bioinformatic prediction of LOY signature (defined by the expression levels of the top 10 Y-linked genes) in various cell subsets, as inferred after deconvolution, showed the presence of the LOY signature in the HSC and HSC-like subsets but not in T cells or other immune cells of the same pts. This was validated by CITE sequencing in 6 LOY AML BM samples where the expression of the Y-linked genes was assessed in both CD34+CD33+HLA-DR+ and CD3+TCRαβ+CD4+or CD8+ cells.Collectively, these findings redefine LOY AML as a distinct entity characterized by reduced inflammation, immune evasion, and an age-dependent impact on prognosis. The survival advantage of younger LOY pts and the adverse influence of high Y chromosome expression in CN-AML underscore the need to recognize Y chromosome biology as a possible determinant of outcome and therapeutic vulnerability in AML.