High‐Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures

The synapse, which represents the structural and functional basis of neuronal communication, is one of the first elements affected in several neurodegenerative diseases. To better understand the potential role of gene expression in synapse loss, we developed an original high‐content screening (HCS) model capable of quantitatively assessing the impact of gene silencing on synaptic density. Our approach is based on a model of primary neuronal cultures (PNCs) from the neonatal rat hippocampus, whose mature synapses are visualized by the relative localization of the presynaptic protein Synaptophysin with the postsynaptic protein Homer1. The heterogeneity of PNCs and the small sizes of the synaptic structures pose technical challenges associated with the level of automation necessary for HCS studies. We overcame these technical challenges, automated the processes of image analysis and data analysis, and carried out tests under real‐world conditions to demonstrate the robustness of the model developed. In this article, we describe the screening of a custom library of 198 shRNAs in PNCs in the 384‐well plate format. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Culture of primary hippocampal rat neurons in 384‐well plates Basic Protocol 2: Lentiviral shRNA transduction of primary neuronal culture in 384‐well plates Basic Protocol 3: Immunostaining of the neuronal network and synaptic markers in 384‐well plates Basic Protocol 4: Image acquisition using a high‐throughput reader Basic Protocol 5: Image segmentation and analysis Basic Protocol 6: Synaptic density analysis