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Version 1.0. Last Updated: June 11, 2025

Web-Enabled Molecular Systems Architecture of Periodontitis

Supplementary Information To
Molecular Systems Architecture of Host-Microbiome Interactions in Periodontitis

V.A. Shiva Ayyadurai^1,2, Prabhakar Deonikar^1,2 & Philip Stashenko^3
1Systems Biology Group, CytoSolve Research Division, CytoSolve, Inc., Cambridge, MA
²Open Science Institute, International Center for Integrative Systems, Cambridge, MA
³Departments of Translational Dental Medicine and Departmetn of Endodontics, Goldman School of Dental Medicine, Boston University, Boston, MA

Summary

Periodontitis is a complex, multifactorial disease arising from disruptions in host-microbiome homeostasis, leading to inflammation, soft-tissue degradation, and alveolar bone loss. This study employs a systems biology approach using the CytoSolve® computational platform to develop a comprehensive molecular systems architecture that elucidates the interactive signaling pathways among microbial, immune, and host periodontal cell types. A systematic review of literature spanning 1980–2022 curated data on eight key cell types involved in the periodontitis microenvironment: gingival epithelial cells, fibroblasts, periodontal ligament cells, endothelial cells, keratinocytes, immune cells, bone cells, and microbial cells.

The study maps 14 molecular systems implicated in periodontitis, focusing on key pathways such as IL-8, IL-6, TLR4, C5aR, RANKL, and gingipain-mediated signaling. Porphyromonas gingivalis is identified as a keystone pathogen that modulates host signaling to evade immune clearance, inhibit neutrophil function, and enhance osteoclastogenesis via RANKL upregulation. The architecture reveals critical crosstalk that leads to immune dysregulation, soft-tissue loss, and bone resorption.

The resulting three-layered architecture offers a visual and mechanistic framework for understanding disease progression and identifying therapeutic targets. It enables identification of intervention points that may inhibit inflammation, promote tissue preservation, and restore homeostasis. The study sets the stage for future in silico modeling and open-source collaborative research in periodontitis, and proposes this systems architecture as a foundational tool for drug development and personalized therapeutic strategies.

Periodontal cellular environment. The microbiome interacts with cells from the soft and hard tissues leading to the pathogenesis of periodontitis. An imbalance in the oral microbiome stimulates the activation of immune cells, mediating the degradation of soft and hard tissue.

 A. Schematics of interactive signaling among microbiome cells and soft- and hard-tissue cells derived from the CytoSolve bioinformatics process. B. Interactions among the microbiome, epithelial cells, and neutrophils leading to immune system modulation. C. Interactions between the microbiome and epithelial cells leading to soft-tissue loss.

 D. Interactions among the microbiome (represented by P gingivalis), immune cells (represented by macrophage), and hard tissue (represented by osteoclast, leading to hard-tissue loss). E. p38 mitogen-activated protein kinases signaling in neutrophils leads to immune activation. F. Interactions between the microbiome and epithelial cells leading to soft-tissue loss.G. Interactions between the microbiome and gingival fibroblasts leading to soft-tissue loss

H. Interactions among the microbiome, soft tissue, and hard tissue leading to bone loss