Combinatorial Cell-Adhesion and Activity Codes Instruct Cortical Modality Identity
The emergence of functional sensory modalities requires precise cortical arealization and appropriate thalamocortical targeting. Although early morphogen gradients set broad cortical territories, the mechanisms that specify sensory identity and guide modality-specific thalamocortical targeting remain unknown. Here, we identify an embryonic set of activity-independent cortical "protogenes", prominently enriched for cell-adhesion molecules, that are differentially expressed between primary somatosensory (S1) and visual (V1) cortices prior to thalamic innervation. These adhesion programs are selectively localized to layer 4, the main thalamo-recipient layer, and strikingly mirror the adhesion profiles of their corresponding thalamic nuclei, suggesting partner recognition. Disrupting thalamic activity alters modality-specific spontaneous cortical dynamics and the postnatal expression of another set of modality-specific genes, indicating a modulatory role for thalamic activity in cortical identity. These findings support a two-step model in which cortical identity is primed by adhesion codes driving modality-specific thalamocortical targeting, and later refined by patterned thalamic activity to establish functional cortical modalities.