A Pilot Network-Based Analysis Reveals HPV Genotype-Associated Microbiome Dysbiosis Signatures in Juvenile-Onset Recurrent Respiratory Papillomatosis: Hypothesis-Generation for Ecological Dynamic Studies.
Juvenile-Onset Recurrent Respiratory Papillomatosis (JORRP) is driven by HPV6 and HPV11, yet viral aetiology alone cannot explain its extreme clinical heterogeneity and unpredictable recurrence. While the virus initiates the disease, the laryngeal microbiome may act as an unexplored ecological modulator associated with disease severity and recurrent patterns. We aimed to characterize the metabolically active laryngeal microbiome and its functional interactome to identify ecological signatures associated with JORRP chronicity. We conducted a retrospective compositional analysis of the active laryngeal microbiome using 27 formalin-fixed paraffin-embedded (FFPE) papilloma biopsies. Captured cDNA was sequenced via 16S rRNA (V1-V3) amplicon sequencing. Advanced Compositional Data Analysis (CoDA) frameworks, including ALDEx2 for differential abundance, Random Forest with Boruta feature selection, and robust ensemble network inference, were employed alongside functional predictions (PICRUSt2) to evaluate ecological restructuring across disease severity, HPV genotypes, and surgical resection burden. Distinct microbial signatures were associated with clinical outcomes. Nominally enriched genera and machine learning models identified Moraxella, Propioniciclava, and Prevotella as exploratory candidate biomarkers, with the Random Forest model achieving a high discriminatory power (AUC = 1.0 for Papilloma Severeness). HPV11 infection showed a trend toward marked reduction in network connectivity compared to other genotypes. Aggressive phenotypes were identified by a fragmented interactome dominated by isolated pathogenic modules anchored by Leptotrichia and Aerococcus, and a highly metabolically enriched functional profile in aerobic respiration and siderophore-mediated iron acquisition. In contrast, non-aggressive lesions retained cohesive, modular homeostasis anchored by environmental commensals. JORRP pathogenesis extends beyond viral infection to encompass a profound ecological restructuring of the laryngeal microbiome. Aggressive disease and HPV11 infection are distinctly characterized by severe network disassembly and the expansion of isolated, metabolically enriched dysbiotic modules. These exploratory topological and predictive signatures suggest that JORRP involves ecosystem-level dysbiosis, providing a foundation for future ecological dynamic studies and identifying candidate biomarkers warranting prospective validation.
Juvenile-Onset Recurrent Respiratory Papillomatosis (JORRP) is driven by HPV6 and HPV11, yet viral aetiology alone cannot explain its extreme clinical heterogeneity and unpredictable recurrence. While the virus initiates the disease, the laryngeal microbiome may act as an unexplored ecological modulator associated with disease severity and recurrent patterns. We aimed to characterize the metabolically active laryngeal microbiome and its functional interactome to identify ecological signatures associated with JORRP chronicity. We conducted a retrospective compositional analysis of the active laryngeal microbiome using 27 formalin-fixed paraffin-embedded (FFPE) papilloma biopsies. Captured cDNA was sequenced via 16S rRNA (V1-V3) amplicon sequencing. Advanced Compositional Data Analysis (CoDA) frameworks, including ALDEx2 for differential abundance, Random Forest with Boruta feature selection, and robust ensemble network inference, were employed alongside functional predictions (PICRUSt2) to evaluate ecological restructuring across disease severity, HPV genotypes, and surgical resection burden. Distinct microbial signatures were associated with clinical outcomes. Nominally enriched genera and machine learning models identified Moraxella, Propioniciclava, and Prevotella as exploratory candidate biomarkers, with the Random Forest model achieving a high discriminatory power (AUC = 1.0 for Papilloma Severeness). HPV11 infection showed a trend toward marked reduction in network connectivity compared to other genotypes. Aggressive phenotypes were identified by a fragmented interactome dominated by isolated pathogenic modules anchored by Leptotrichia and Aerococcus, and a highly metabolically enriched functional profile in aerobic respiration and siderophore-mediated iron acquisition. In contrast, non-aggressive lesions retained cohesive, modular homeostasis anchored by environmental commensals. JORRP pathogenesis extends beyond viral infection to encompass a profound ecological restructuring of the laryngeal microbiome. Aggressive disease and HPV11 infection are distinctly characterized by severe network disassembly and the expansion of isolated, metabolically enriched dysbiotic modules. These exploratory topological and predictive signatures suggest that JORRP involves ecosystem-level dysbiosis, providing a foundation for future ecological dynamic studies and identifying candidate biomarkers warranting prospective validation.