Network analysis and species-specific siRNA design targeting MMP7 in feline chronic kidney disease

Abstract

Chronic kidney disease (CKD) is a common acquired disorder in older cats and is associated with tubulointerstitial fibrosis, chronic inflammation, hypoxia, oxidative stress, and extracellular matrix (ECM) remodeling. Matrix metalloproteinase-7 (MMP7), a tubular epithelial-derived endopeptidase, has been implicated in renal fibrotic progression in human and rodent CKD, but remains poorly characterized in Felis catus. This study aimed to characterize the MMP7-associated molecular network in feline CKD and to design species-specific small interfering RNA (siRNA) candidates targeting Felis catus MMP7 using a multi-step in silico workflow. A 27-gene candidate panel representing ECM remodeling, fibrosis, hypoxia, inflammation, inflammasome activation, apoptosis, oxidative stress, and tubular injury was analyzed using Enrichr, STRING v12.0, Cytoscape v3.10.4, and cytoHubba. Functional enrichment analyses showed significant associations with inflammatory and cytokine signaling, ECM organization and degradation, collagen metabolism, and chemical stress response. STRING analysis yielded a highly interconnected protein-protein interaction (PPI) network of 26 mapped nodes and 125 edges, with significant PPI enrichment (p < 1.0 × 10−16). Although MMP7 was not among the top global hubs, it was positioned within an ECM remodeling submodule involving MMP2, MMP9, TIMP1, CCN2, COL1A1, and TGFB1. Using the Felis catus MMP7 Reference Sequence (RefSeq) transcript XM_003992303.3, four coding sequence-targeting siRNA candidates were initially selected, and two were prioritized. MMP7-siRNA1 showed the most favorable overall profile, including a comparatively favorable Basic Local Alignment Search Tool (BLAST)-based specificity profile, stable duplex formation, low self-folding tendency, and high thermal stability. Together, these findings prioritize MMP7-siRNA1 as the primary candidate for experimental evaluation and support species-specific MMP7 targeting as a testable approach for investigating renal matrix remodeling in feline CKD.