Development of a cell-defined siRNA microarray for analysis of gene function in human bone marrow stromal cells

Abstract

Small interfering RNA (siRNA) screening approaches have provided useful tools for the validation of genetic functions; however, image-based siRNA screening using multiwell plates requires large numbers of cells and time, which could be the barrier in application for gene mechanisms study using human adult cells. Therefore, we developed the advanced method with the cell-defined siRNA microarray (CDSM), for functional analysis of genes in small scale within slide glass using human bone marrow stromal cells (hBMSCs).We designed cell spot system with biomaterials (sucrose, gelatin, poly-l-lysine and matrigel) to control the attachment of hBMSCs inside spot area on three-dimensional (3D) hydrogel-coated slides. The p65 expression was used as a validation standard which described our previous report. For the optimization of siRNA mixture, first, we detected five kinds of commercialized reagent (Lipofectamine 2000, RNAi-Max, Metafectine, Metafectine Pro, TurboFectin 8.0) via validation. Then, according to quantification of p65 expression, we selected 2μl of RNAi-Max as the most effective reagent condition on our system. Using same validation standard, we optimized sucrose and gelatin concentration (80mM and 0.13%), respectively. Next, we performed titration of siRNA quantity (2.66–5.55μM) by reverse transfection time (24h, 48h, 72h) and confirmed 3.75μM siRNA concentration and 48h as the best condition. To sum up the process for optimized CDSM, 3μl of 20μM siRNA (3.75μM) was transferred to the 384-well V-bottom plate containing 2μl of dH2O and 2μl of 0.6M sucrose (80mM). Then, 2μl of RNAi-Max was added and incubated for 20min at room temperature after mixing gently and centrifugation shortly. Five microliters of gelatin (0.26%) and 2μl of growth factor reduced phenol red-free matrigel (12.5%) were added and mixed by pipetting gently. Finally, optimized siRNA mixture was printed on 3D hydrogel-coated slides and cell-defined attachment and siRNA reverse transfection were induced.The efficiency of this CDSM was verified using three siRNAs (targeting p65, Slug, and N-cadherin), with persistent gene silencing for 5days. We obtained the significant and reliable data with effective knock-down in our condition, and suggested our method as the qualitatively improved siRNA microarray screening method for hBMSCs.