Single-cell transcriptomic analysis reveals ifng/IL-6-mediated inflammatory networks in der(1;7)(q10;p10) Myelodysplastic Syndromes

Abstract Background: Der(1;7)(q10;p10)[der(1;7)] as a recurrent unbalanced translocation in MDS has steadily gained attention. The direct consequence of this karyotype alteration is +1q and 7q-;however, accumulating evidence supports that der(1;7) is distinct from 7q- in clinical and molecular features, representing a unique MDS subtype. However, the transcriptomic features of these patients remain largely unknown. Although previous bulk-RNA seq results have revealed dysregulated oncogene and tumor suppressor gene expression due to dosage effects in der(1;7) MDS, the limitations of bulk sequencing technology prevent direct association of these findings with der(1;7)-aberrant cells. In this study, we applied scRNA-seq in der(1;7) MDS to perform in-depth analysis at single-cell resolution, providing novel insights into der(1;7) hematopoietic development, disease progression mechanisms, and key molecular pathways. Methods: This study analyzed bone marrow mononuclear cells (BMMCs) using bulk RNA-seq and 10X scRNA-seq approaches. Bulk RNA-seq was performed on 156 MDS patients, including 7 cases with der(1;7), while scRNA-seq was conducted on 4 der(1;7) MDS cases, 2 secondary acute myeloid leukemia (sAML) cases with der(1;7), 3 healthy donors, and 2 MDS patients with normal karyotypes as controls. We utilized the CopyKat algorithm to identify cells harboring der(1;7) and CellChat was used to characterize the intercellular communication networks. Results: Principal component analysis (PCA) of transcriptomic data from MDS patients with different karyotypes revealed that der(1;7) MDS patients clustered more tightly, indicating relatively reduced internal heterogeneity and distinct gene expression patterns. Enrichment analysis of the top 100 genes with the most negative loadings on PC1 revealed that inflammatory activation and immune dysregulation are characteristic changes in der(1;7) MDS. At single-cell resolution, we observed that overexpressed genes in most der(1;7) positive cell subsets were enriched in multiple inflammation- and immune-related pathways, with interferon-mediated inflammatory pathways being particularly prominent. Notably, we observed similar results in CNV neutral cells[der(1;7) WT], suggesting that inflammatory pathway activation may result from bone marrow microenvironment remodeling mediated by pro-inflammatory factors such as IFN and IL-6. Given the importance of IFN-γ and IL-6 in der(1;7) MDS, we identified IFN-γ primarily originated from CD8+ effector T cells in der(1;7) MDS, and the EGR1+ ACB as the main cell subset with detectable IL-6 expression. Similar to recent findings in iMCD, we discovered that monocytes in der(1;7) MDS, particularly der(1;7)-positive subsets, receive IL-6 signals from B cells and IFN-γ signals from T cells, with higher IL-6 and IFN-γ response pathway activities accompanied by elevated cytokine production and inflammatory pathway scores. 1q gain played a crucial role in this process, not only enhancing sensitivity to pro-inflammatory signals through upregulation of IL-6R (1q21) expression but also further amplifying pro-inflammatory effects through upregulation of S100A family genes expression(1q21). The stability of gene dosage effects caused by der(1;7) karyotype during progression implies that advancement is not driven by additional cytogenetic evolution, but by the amplification of effects under selective pressure. The anti-apoptotic gene MCL1 located on 1q showed upregulation compared to CNV neutral cells across different stages in der(1;7) patients, suggesting that these anti-apoptotic properties conferred by 1q gain may be important intrinsic factors for der(1;7) cells competitive advantage in the inflammatory microenvironment. Conclusion: This study, our comprehensive analysis reveals the critical role of IFNG/IL-6-mediated inflammation in der(1;7) MDS and identifies a special pro-inflammatory network in BM microenvironment remodeling. Additionally, we demonstrate the importance of 1q gain in maintaining der(1;7) clonal dominance, which represents a potential therapeutic vulnerability.