Multi-omics unveils ER stress-driven pDC-like leukemia stem cells in pDC-AML

Abstract Introduction: Acute myeloid leukemia (AML) is characterized by aggressive proliferation, differentiation blockage, and heterogeneous genetic abnormalities, which significantly impact clinical outcomes. In 2022, the WHO recognized that some AML patients exhibit clonally expanded plasmacytoid dendritic cells (pDC-AML), associated with poor prognosis and unique immunophenotypic and molecular features. However, the role of these pDCs and the underlying pathogenetic mechanisms remain largely unexplored. This study presents the first multi-omics analysis aimed at investigating the clinical, proteomic, transcriptomic features and underlying pathogenetic mechanisms of pDC-AML. Methods: From October 2017 to October 2023, 18 pDC-AML patients were enrolled. During the same period, 69 age- and gender-matched non-pDC-AML and 16 BPDCN patients (from July 2014 to October 2023) were included as control groups. Data-independent acquisition (DIA) proteomics, 10X Genomics single-cell RNA sequencing (scRNA-seq), and immune repertoire sequencing were performed on bone marrow (BM) samples from 8 pDC-AML, 5 non-pDC-AML, 1 BPDCN patient, and 9 healthy donors (HDs). Follow-up continued through March 25, 2025. The study adhered to the Declaration of Helsinki and was approved by the Medical Ethics Committee of Tongji Hospital (TJ-IRB202404059). Results: We observed a chemotherapy response rate of 39% (7/18) in pDC-AML patients, significantly lower than the 82.6% (57/69) in non-pDC-AML patients. Compared with non-pDC-AML patients, pDC-AML patients showed significantly worse overall survival (OS: 32.0 months vs. 11.0 months) and progression-free survival (PFS: 31.0 months vs. 5.5 months), while no significant difference in OS and PFS between the two groups of patients receiving HSCT. scRNA-seq identified a distinct pDC-like leukemic stem cell (LSC) subcluster in the bone marrow of pDC-AML, marked by the co-expression of hematopoietic stem cell (HSC) and pDC markers (CD34, CD33, CD133, CD123, BDCA-2, BDCA-4, TLR9) along with pDC differentiation transcription factors (FLT3, PU.1, IRF8, TCF4, BCL11A). Prognostic analysis from the TCGA-LAML cohort showed that AML blasts highly expressing this pDC-like LSC signature correlated with poorer OS. Notably, a gradual increase in ERS signaling was observed along the LSC-to-pDC trajectory, suggesting a potential regulatory role of ERS in this differentiation process. Further analysis demonstrated that compared to non-pDC-AML, pDC-AML-derived pDCs exhibited higher expression of CD34, precursor pDC markers (IRF8, BCL11A, TCF4), and the clonal pDC marker SPIB. Functional pathways, including type I interferon production and T cell activation, were significantly downregulated, while ERS pathways were markedly upregulated, while the functional marker ILT7 was downregulated. Immune repertoire sequencing revealed impaired immune responses in pDC-AML, with reduced T/B cell clonal diversity. In one MRD+ patient, residual pDCs persisted post-treatment, showing sustained ERS activation. Proteomic analysis confirmed the upregulation of ERS-related proteins (HSPA5, HSPA9, SEC16A, and PDIA3) in the bone marrow of pDC-AML patients. In vitro, the activation of the ERS pathway by tunicamycin in AML cell lines led to significant upregulation of the pDC transcription factor BCL11A and surface pDC markers (CD123, BDCA2, HLA-DR, CD4), together confirming the role of ERS in the differentiation and functional regulation of pDC-like LSCs in pDC-AML, reinforcing the potential therapeutic implications of targeting the ERS pathway. Conclusions: This study provides, for the first time, a comprehensive multi-omics landscape of pDC-AML, revealing that AML patients with clonally expanded pDCs represent a distinct subtype characterized by unique clinical, proteomic, and transcriptomic features. Notably, it identifies a specific pDC-like LSC cluster, upregulated ERS pathways, and a dysfunctional T and B cell state, which present promising targets for therapeutic intervention.