AAV-Cre induces dose-dependent neurotoxicity and focal neuronal lesions

Lesion studies remain central to neuroscience, offering key insights into brain–behavior relationships and the consequences of permanent neuronal loss. Excitotoxic agents, though widely used, can produce variable lesion extent and lack cell-type specificity. There remains a need for robust and controlled approaches to induce persistent neuronal loss in defined brain regions and neuronal populations. Here, we characterize Cre recombinase expression as a reproducible approach for inducing focal neuronal lesions in mice. Using high-titer adeno-associated viral (AAV) vectors, we show that Cre expression induces focal neurodegeneration across brain regions, with neuronal loss observed in both excitatory and inhibitory neuronal population. This effect is observed across different viral serotypes and independently of fluorescent tags, and is not readily detectable with standard DAPI staining but is revealed by neuronal markers. The resulting neuronal loss is followed by glial remodeling and significant behavioral alterations. These findings also emphasize that high levels of Cre expression should be used cautiously in experiments intended to preserve neuronal integrity, as Cre-induced toxicity may represent an important experimental confound. Conversely, when neuronal loss is intended, AAV-mediated Cre expression provides a genetically targeted approach for producing persistent neuronal lesions, complementary to existing lesion methods.