Abstract
Introduction Histiocytic neoplasms are rare hematological disorders characterized by clonal proliferation of myeloid-derived cells. While genomic studies have identified recurrent MAPK and PI3K pathway mutations, the functional proteomic landscape of these diseases remains poorly characterized. Proteomic profiling provides a complementary layer of information for biological pathway activation, cytokine secretion, and microenvironmental interactions that extend beyond genomic and transcriptomic data.
Objectives To conduct an in-depth proteomic analysis of plasma and tissue samples from patients with histiocytic neoplasms, including Erdheim-Chester Disease (ECD), Langerhans Cell Histiocytosis (LCH), and Rosai-Dorfman Disease (RDD), to uncover disease-specific signatures, identify candidate biomarkers, and gain mechanistic insights that may support improved diagnosis, patient stratification, and targeted therapeutic approaches.
Methods We applied the Seer Proteograph™ XT Assay, a nanoparticle-based technology enabling unbiased enrichment of thousands of plasma proteins, followed by mass spectrometry analysis. Plasma samples were obtained from 9 patients with ECD and 9 healthy controls. Additionally, formalin-fixed paraffin-embedded (FFPE) tissue samples from ECD, LCH, and RDD patients were analyzed to evaluate proteomic differences between histiocytoses subtypes. Bioinformatic analysis for differential expression and pathway enrichment analyses were performed to stratify patients and identify biologically relevant signatures.
Results Plasma proteomic profiling revealed over 3,000 significantly differentially expressed proteins (FDR<0.05, fold change >2) in ECD compared to healthy controls. Principal component analysis (PCA) demonstrated clear clustering of ECD versus controls. Further stratification of ECD patients by CNS involvement (based on clinical symptoms and brain MRI findings) uncovered distinct proteomic signatures with unique plasma proteins that were significantly altered between patients with and without CNS involvement, suggesting the feasibility of non-invasive biomarkers for neuro-involvement.
Tissue proteomic analysis across ECD, LCH, and RDD revealed disease-specific enrichment patterns. LCH lesions were enriched for proteins involved in antigen presentation and neutrophil activation, whereas ECD lesions displayed upregulation of metabolic and cytoskeletal pathways. RDD lesions demonstrated a distinct signature enriched for phagocytic and immune regulatory proteins. These profiles align with the immunopathological features of each entity and offer mechanistic insights beyond genomic and epigenomic data.
Among proteins that were found to overlap in both plasma and tissue samples, we found regulators of immune signaling, extracellular matrix and cell adhesion, and developmental pathways, suggesting they may serve as systemic surrogates for local disease activity. In addition, CXCL10 (also known as IP-10), a chemokine implicated in T-cell recruitment and interferon-γ–mediated immune activation was found to be upregulated in ECD patients. This observation is consistent with our previous findings of reduced miR-15 levels in ECD patients - a microRNA that negatively regulates CXCL10 expression - thereby strengthening the biological relevance of our proteomic data and supporting a mechanistic link between epigenetic dysregulation and the inflammatory milieu in ECD.Conclusions: This study comprehensively shows profiles of both plasma and tissue proteomes in histiocytic neoplasms using advanced nanoparticle-based proteomic technology. Our results identify disease-specific protein signatures and candidate biomarkers that may enhance diagnostic precision - particularly in CNS-involved ECD. The integration of proteomics into genomic, epigenomic and clinical data may provide further understanding of disease mechanisms, advancements in personalized care, and minimally invasive diagnostics in histiocytic disorders.
