Single-Cell Transcriptomic Analysis Reveals Distinct Hematopoietic Landscapes and Immune Dysregulation in Der(1;7)(q10;p10) Myelodysplastic Syndromes

Background: Der(1;7)(q10;p10) [der(1;7) ] is a distinct unbalanced translocation mainly observed in myeloid neoplasms, particularly in myelodysplastic syndromes (MDS). This chromosomal aberration l results in monosomy 7q and gain of 1q. Unlike other -7/7q- patients, der(1;7) MDS patients exhibit unique genetic and clinical characteristics. However, the transcriptomic features of these patients remain largely unknown. Previous bulk RNA sequencing studies have revealed differentially expressed genes and signaling pathways based on the analysis of mixed-cell populations, which may not truly reflect the specific transcriptomic signatures of der(1;7) abnormality. In this study, we employed single-cell RNA sequencing (scRNA-seq) to overcome this defect and provide a more comprehensive characterization of the transcriptomic landscape associated with der(1;7) abnormality.

Methods: This study performed 10X scRNA-seq of bone marrow mononuclear cells (BMMCs) obtained from 4 cases of der(1;7) MDS and 2 cases of secondary acute myeloid leukemia (sAML) with der(1;7) abnormality. Additionally, we collected BMMCs from 3 healthy donors and 2 MDS patients with normal karyotypes as controls. The CopyKat algorithm was used to identify cells harboring der(1;7) karyotype abnormality and performed in-depth analyses to investigate the transcriptomic alterations associated with this abnormality and its impact on the hematopoietic system. Furthermore, we compared the transcriptomic features of hematopoietic stem/progenitor cells (HSPCs) and changes in the immune microenvironment during the progression from MDS to sAML.

Results: Employing the CopyKat algorithm, we successfully identified cells with der(1;7) abnormality and observed their distribution within the hematopoietic stem cell (HSC) population, confirming that this karyotype aberration occurs at the primitive stage of hematopoiesis. Although HSC/HSPC with der(1;7) retained their differentiation capacity, they exhibited significant impairment in lymphoid differentiation.

Moreover, we discovered two different types of der(1;7) MDS patients with distinct cellular subpopulation structures: those with der(1;7) as the sole abnormality [der(1;7) sole] and those with der(1;7) co-occurring with trisomy 8. Similar phenomena were observed in sAML. We speculate that different cytogenetic states of der(1;7) may be associated with distinct disease progression patterns. We performed the subpopulation analysis on HSC/HSPCs to validate this finding. Firstly, patients with co-occurring trisomy 8 abnormality showed more significant upregulation of genes located on chromosome 8. Secondly, enrichment analysis found striking differences in biological pathways between patients with der(1;7) abnormality states. Patients with co-occurring trisomy 8 exhibited activation of numerous inflammation-related pathways, such as the NF-kB pathway, while der(1;7) sole MDS patients primarily displayed active cell cycle and DNA damage repair pathways. Interestingly, regardless of the cytogenetic state in MDS, cellular pathways underwent significant alterations upon progression to AML. For instance, der(1;7) sole MDS switched to activation of ribosomal pathways during the AML stage.

We further explore the roles of T cells and NK cells in the progression of the disease. Overall, the composition of T cells and NK cells in der(1;7) sole patients resembled that of normal controls, while patients with co-occurring trisomy 8 exhibited a contraction of the CD4+ T cells and an expansion of the NK cells. Furthermore, we observed a significant alteration in the ratio between the proportion of GZMH-high CD8+ effector T cells(CD8+ Te) and those with high GZMK expression. Regardless of the cytogenetic state in MDS, this ratio decreased by approximately 40% upon progression to AML. We further found that GZMH-high CD8+ Te exhibited enhanced cytotoxicity, whereas GZMK-high CD8+ Te showed characteristics of exhaustion and dysfunction. This shift suggests that alterations in immune homeostasis may play a role in the disease progression of MDS with der(1;7) abnormality.

Conclusion: This study, for the first time, elucidates the hematopoietic structure and intrinsic heterogeneity of der(1;7) MDS through scRNA-seq and reveals potential transcriptomic alterations associated with pathogenesis and disease progression.