FAMSi: A Synthetic Biology Approach to the Fast Assembly of Multiplex siRNAs for Silencing Gene Expression in Mammalian Cells

Abstract RNA interference (RNAi) is mediated by ∼21nt short-interfering double-stranded RNA (siRNA) and shows great promise in delineating gene functions and in developing therapeutics for human diseases. However, effective gene silencing usually requires the delivery of multiple siRNAs for a given gene, which is often technically challenging and time-consuming. Here, by exploiting the Type IIS restriction endonuclease-based synthetic biology methodology, we developed the f ast a ssembly of m ultiplex si RNAs (FAMSi) system. In our proof-of-concept experiments, we demonstrated that multiple fragments containing three, four, or five siRNA sites targeting common Smad4, and/or BMPR-specific Smad1, Smad5, and Smad8 required for BMP9 signaling could be assembled efficiently. The constructed multiplex siRNAs effectively knocked down the expression of Smad4 and/or Smad1, Smad5, and Smad8 in mesenchymal stem cells (MSCs), and inhibited all aspects of BMP9-induced osteogenic differentiation in bone marrow mesenchymal stem cells (BMSCs), including decreased expression of osteogenic regulators/markers, reduced osteogenic marker ALP activity, and diminished in vitro matrix mineralization and in vivo ectopic bone formation. Collectively, we demonstrate that the engineered FAMSi system provides a fast-track platform for assembling multiplexed siRNAs in a single vector, and thus may be a valuable tool to study gene functions or to develop novel siRNA-based therapeutics.