Transcriptomic analysis of perirhinal and lateral entorhinal cortex sub-regions in male mice

The perirhinal cortex (PER) is crucial for object recognition memory and is divided into areas 35 and 36, which have distinct cytoarchitectural and connections. The lateral entorhinal cortex (LEC), subdivided into dorsolateral (DLE) and ventral intermediate (VIE) regions, processes visual and spatial information, projecting it to the hippocampus. However, molecular studies that separately analyze these regions and their cellular populations are lacking, which hinders the identification of marker genes and the understanding of their molecular profiles. In this context, our study investigated the molecular profile of the aforementioned regions using male C57BL/6 mice whose samples were subjected to laser microdissection (LCM). Areas 35 and 36 of the PER and the DLE and VIE subregions of the LEC were isolated and submitted to RNA-seq analysis. Sequencing read alignment was performed using the STAR package, and statistical analysis was carried out with the DESeq2 package to estimate gene expression in the regions of interest. The results were divided into two parts. First, areas 35 and 36 of the PER were analyzed separately, revealing 1 differentially expressed gene between A35 and A36, 167 between A35 and DLE, 708 between A36 and DLE, 693 between VIE and DLE, 1,154 between A35 and VIE, and 1,591 between A36 and VIE. In the second part, areas 35 and 36 were considered as a single PER region, identifying 657 differentially expressed genes between PER and DLE and 1,878 between PER and VIE. Greater segregation of the transcriptomic profile was found between physically distant regions (areas 35 and 36 vs. VIE, DLE vs. VIE) compared to physically closer regions (A35 vs. A36; areas 35 and 36 vs. DLE). Additionally, our transcriptomic analysis identified potential marker genes for PER (6 genes more highly expressed in PER compared to LEC subregions), DLE (4 genes more highly expressed in DLE compared to PER and VIE), and VIE (8 genes more highly expressed in VIE compared to PER). In silico analysis showed shared enrichment of neuroactive ligand receptor interaction pathway in all comparisons, considering PER areas both separately and together. In the comparison between areas 35 and 36 with LEC, there was higher expression of genes encoding receptors of melanocortin, leptin, and glucagon, suggesting that PER, compared to LEC, would be more sensitive to these hormones and participate of nutritional status of the organism. There was also higher expression of genes associated with axonal guidance of glutamatergic neurons in DLE compared to VIE, which may be linked to an increased neuroplasticity mechanisms pro-excitability in the dorsal LEC region. Supporting this hypothesis, higher expression of the genes BDNF , GDFN α1 receptor were observed in DLE compared to VIE. Thus, our study is the first to show the molecular differences in areas 35 and 36 of the PER and the DLE and VIE subregions of the LEC. These findings may contribute to the understanding of these regions and the identification of specific molecular markers for cellular populations, helping to infer possible functional roles of these populations based on the molecular profile identified.