Network medicine modeling of the m⁶A regulatory landscape identifies a KLF6-WTAP axis as a therapeutic target in pulmonary fibrosis

Xu, Chengyuan and Zhou, Ziheng and Lin, Yani and Zhang, Siqi and Cai, Shanshan and Li, Bing and Wang, Zhifang (2026) Network medicine modeling of the m⁶A regulatory landscape identifies a KLF6-WTAP axis as a therapeutic target in pulmonary fibrosis. Journal of Translational Medicine. ISSN 1479-5876

Abstract

Background Idiopathic pulmonary fibrosis (IPF) is sustained by multicellular circuits linking endothelial activation, fibroblast remodeling, and immune crosstalk. However, how N⁶-methyladenosine (m⁶A) regulation is embedded within these networks and how such network-level regulators can be prioritized as actionable nodes relevant to clinical pharmacology and safety remains unclear. Methods Guided by a computational modelling and network medicine framework, we integrated single-cell RNA-seq with spatial transcriptomics to systematically profile 23 canonical m⁶A regulators in pulmonary fibrosis and to map their coupling to immune, cytokine, and extracellular-matrix (ECM) programs. CellChat-based ligand–receptor inference was used to reconstruct intercellular communication, while hdWGCNA co-expression modules and pseudotime trajectories resolved intracellular program architecture and dynamic transitions. Key nodes were further interrogated experimentally. WTAP function was evaluated via shRNA-mediated silencing in primary human lung fibroblasts and fibroblast-specific conditional deletion in a bleomycin (BLM)–induced mouse fibrosis model. Immunofluorescence, MeRIP-qPCR, ChIP-qPCR, luciferase reporter assays, RT-qPCR, and western blotting were used to validate WTAP expression, upstream regulation, and downstream m⁶A-linked effects. Results Network modelling highlighted IGF2BP3-associated sprouting angiogenesis with strengthened adhesion/chemokine signaling in endothelial cells and identified HNRNPA2B1 as a marker of pro-inflammatory macrophage states characterized by enhanced MDK and ITGB2 axes. In fibroblasts, WTAP emerged as a central m⁶A writer connecting an ECM/contractile module to a metabolic-to-mechanical transition along pseudotime. Spatial mapping and immunofluorescence confirmed elevated WTAP in fibroblast-enriched fibrotic regions. Functionally, WTAP silencing attenuated TGF-β–induced α-SMA and collagen III expression, reduced proliferation/migration, and lowered global m⁶A levels. Mechanistically, ChIP-qPCR and promoter reporter assays supported KLF6-dependent transcriptional activation of WTAP, and WTAP was associated with methylation-linked regulation of MYC, NR4A3, and IGFBP5. In vivo, fibroblast-specific WTAP deletion improved survival, preserved lung mechanics, and diminished collagen burden in BLM-treated mice. Conclusions This study establishes a multi-omics network medicine map of m⁶A regulation in IPF and nominates the KLF6–WTAP axis as a central, potentially targetable hub coordinating pathogenic stromal programs. The framework provides a systems-level basis for target prioritization and for evaluating fibrosis-related safety liabilities and pharmacovigilance signals in clinical pharmacology.