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Synapses contain hundreds of distinct proteins whose heterogeneous expression levels are determinants of synaptic plasticity and signal transmission relevant to a range of diseases. Here, we use diffusible nucleic acid imaging probes to profile neuronal synapses using multiplexed confocal and super-resolution microscopy. Confocal imaging is performed using high-affinity locked nucleic acid imaging probes that stably yet reversibly bind to oligonucleotides conjugated to antibodies and peptides. Super-resolution PAINT imaging of the same targets is performed using low-affinity DNA imaging probes to resolve nanometer-scale synaptic protein organization across nine distinct protein targets. Our approach enables the quantitative analysis of thousands of synapses in neuronal culture to identify putative synaptic sub-types and co-localization patterns from one dozen proteins. Application to characterize synaptic reorganization following neuronal activity blockade reveals coordinated upregulation of the post-synaptic proteins PSD-95, SHANK3 and Homer-1b/c, as well as increased correlation between synaptic markers in the active and synaptic vesicle zones.

 

Abstract Human induced pluripotent stem cell-derived (iPSC) neural cultures offer clinically relevant models of human diseases, including Amyotrophic Lateral Sclerosis, Alzheimer’s, and Autism Spectrum Disorder. In situ characterization of the spatial-temporal evolution of cell state in 3D culture and subsequent 2D dissociated culture models based on protein expression levels and localizations is essential to understanding neural cell differentiation, disease state phenotypes, and sample-to-sample variability. Here, we apply PR obe-based I maging for S equential M ultiplexing (PRISM) to facilitate multiplexed imaging with facile, rapid exchange of imaging probes to analyze iPSC-derived cortical and motor neuron cultures that are relevant to psychiatric and neurodegenerative disease models, using over ten protein targets. Our approach permits analysis of cell differentiation, cell composition, and functional marker expression in complex stem-cell derived neural cultures. Furthermore, our approach is amenable to automation, offering in principle the ability to scale-up to dozens of protein targets and samples. 

Neuronal synapses transmit electrochemical signals between cells through the coordinated action of presynaptic vesicles, ion channels, scaffolding and adapter proteins, and membrane receptors. In situ structural characterization of numerous synaptic proteins simultaneously through multiplexed imaging facilitates a bottom-up approach to synapse classification and phenotypic description. Objective automation of efficient and reliable synapse detection within these datasets is essential for the high-throughput investigation of synaptic features. Convolutional neural networks can solve this generalized problem of synapse detection, however, these architectures require large numbers of training examples to optimize their thousands of parameters. We propose DoGNet, a neural network architecture that closes the gap between classical computer vision blob detectors, such as Difference of Gaussians (DoG) filters, and modern convolutional networks. DoGNet is optimized to analyze highly multiplexed microscopy data. Its small number of training parameters allows DoGNet to be trained with few examples, which facilitates its application to new datasets without overfitting. We evaluate the method on multiplexed fluorescence imaging data from both primary mouse neuronal cultures and mouse cortex tissue slices. We show that DoGNet outperforms convolutional networks with a low-to-moderate number of training examples, and DoGNet is efficiently transferred between datasets collected from separate research groups. DoGNet synapse localizations can then be used to guide the segmentation of individual synaptic protein locations and spatial extents, revealing their spatial organization and relative abundances within individual synapses. The source code is publicly available: https://github.com/kulikovv/dognet.