Context-tuned strategies for marker selection precision in neuronal studies

Marker selection precision in neuronal studies is critical for reliable neuron identification. However, it largely depends on the experimental context. Variations in neuronal marker specificity across experimental models, neuronal maturation stages, and neurotransmitter phenotypes have highlighted the vitality of implementing “context-tuned” strategies in marker selection. Neuronal markers arise from canonical protein-coding genes, non-coding RNAs (ncRNAs), including microRNAs (miRNAs), isoform-specific variants, neurotransmitters, and numerous metabolic signatures. Here, we emphasize protein-coding genes as markers because of their wide availability, ease of interpretation, and compatibility with standard detection methods like qPCR, in situ hybridization, immunocytochemistry, and Western blotting. They are also directly linked to cellular structures, signaling pathways, functional importance, and are adaptable across different platforms. We aim to guide the strategic selection and application of neuronal markers to maximize accuracy and interpretive confidence across diverse experimental systems. The review addresses the molecular origin and nature of neuronal markers, their specific applications, including distinguishing neuronal from non-neuronal cells in tissue or histological preparations, identifying neurotransmitter phenotypes in neuronal cultures and tissues, evaluating neuronal maturity in progenitor-derived systems, discriminating between immature and fully differentiated neurons in vitro, and detecting neurons alongside other neuronal or non-neuronal subtypes in mixed populations. Furthermore, it emphasizes positive and negative marker strategies, accounting for developmental timing, cellular specificity, model system differences, and rigorous exclusion of unintended cell types. Through this comprehensive review, we deliver a simplified reference for neuroscientists seeking to enhance the accuracy, specificity, and reproducibility of their neurobiological studies.