Targeted genomic DNA sequencing (506-gene panel) and whole-exome sequencing analysis of EBV-positive inflammatory follicular dendritic cell sarcoma

Epstein-Barr virus-positive inflammatory follicular dendritic cell sarcoma (EBV+ IFDCS), recently reclassified in the 5th edition of the WHO classification of lymphoid neoplasms, is a rare mesenchymal and dendritic cell tumor distinct from conventional follicular dendritic cell sarcoma (FDCS) in cellular origin and clinicopathological features. To address this, we present the largest sequencing cohort of EBV+ IFDCS to date, combining targeted next-generation sequencing (NGS) of 12 cases and whole-exome sequencing (WES) of 3 cases. This study aims to elucidate the molecular characteristics of EBV+ IFDCS to better understand its pathogenesis and identify potential therapeutic targets. 12 EBV+ IFDCS cases were analyzed using next-generation sequencing (NGS) with a 506-gene panel, and whole-exome sequencing (WES) was performed on 3 cases. The analysis focused on identifying copy number variations (CNVs), gene fusions, and pathogenic mutations. KEGG pathway analysis was conducted to explore enriched oncogenic pathways. CNV analysis via WES identified focal chromosomal deletions in 2 of 3 cases: 7p and 14q deletions in Case 1, and 17p deletion plus deep deletions in NPRL2 (chromosome 3) and STK11 (chromosome 19) in Case 6. While pathogenic/drug-sensitive SNVs varied across the 12 patients (Fig. 2). Only Patient 3 (48-year-old female, splenic classical subtype EBV+ IFDCS) was TMB-H (11.2 mutations/Mb, ≥ 10 mutations/Mb as threshold), harboring NQO1 p.P187S (VAF = 32.6%) and a germline PKHD1 Class 3 VUS. This case had no unique somatic mutations vs. low-TMB cases, with histological features (fascicular spindle cells, moderate lymphoplasmacytic infiltration) consistent with the classical subtype (Fig. 1A). KEGG pathway analysis revealed enrichment in PI3K-AKT, cell cycle, Notch, and EBV infection pathways. WES of Patients 1, 6, 10 showed TMB-L (1.8–3.5 mutations/Mb); Patient 3’s TMB-H (11.2 mutations/Mb, ≥ 10 mutations/Mb as solid tumor threshold) was validated via targeted NGS (723× coverage). WES of TMB-L cases revealed predominant missense mutations/SNVs (C > T transitions: 50% of SNPs, Fig. 5C), with 3–9 somatic mutations per case and no shared mutations—highlighting potential potential high tumor heterogeneity, further supported by Patient 3’s unique TMB-H phenotype. This study reveals the unique molecular landscape of EBV+ IFDCS, characterized by frequent NQO1 mutations and activation of key oncogenic pathways. These findings provide critical insights into the tumor’s pathogenesis and suggest potential molecular targets for future therapeutic strategies. 1. Frequent NQO1 mutations and PI3K-AKT/Notch pathway enrichment in EBV+ IFDCS suggest key drivers of tumor progression and potential targets. 2. Potential high tumor heterogeneity combined with a low mutational burden suggests unique pathogenesis and may pose challenges for targeted therapies—with confirmation requiring larger WES cohorts.