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. 2022 Oct 3:13:322-329.
doi: 10.1016/j.ibneur.2022.09.009. eCollection 2022 Dec.

The transcriptome of rat hippocampal subfields

João P D Machado  1   2 , Maria C P Athie  3   2 , Alexandre H B Matos  3   2 , Iscia Lopes-Cendes  3   2 , André S Vieira  1   2
Affiliations

The transcriptome of rat hippocampal subfields

João P D Machado et al. IBRO Neurosci Rep. .

Abstract

The hippocampus comprises several neuronal populations such as CA1, CA2, CA3, and the dentate gyrus (DG), which present different neuronal origins, morphologies, and molecular mechanisms. Laser capture microdissection (LCM) allows selectively collecting samples from target regions and eliminating unwanted cells to obtain more specific results. LCM of hippocampus neuronal populations coupĺed with RNA-seq analysis has the potential to allow the exploration of the molecular machinery unique to each of these subfields. Previous RNA-seq investigation has already provided a molecular blueprint of the hippocampus, however, there is no RNA-seq data specific for each of the rat hippocampal regions. Serial tissue sections covering the hippocampus were produced from frozen brains of adult male Wistar rats, and the hippocampal subfields CA1, CA2, CA3, and DG were identified and isolated by LCM. We found evident segregation of the transcriptomic profile from different regions of the hippocampus and the expression of known, as well as novel, specific marker genes for each region. Gene ontology enrichment analysis of CA1 subfield indicates an enrichment of actin regulation and postsynaptic membrane AMPA receptors genes indispensable for long-term potentiation. CA2 and CA3 transcripts were found associated with the increased metabolic processes. DG expression was enriched for ribosome and spliceosome, both required for protein synthesis and maintenance of cell life. The present findings contribute to a deeper understanding of the differences in the molecular machinery expressed by the rat hippocampal neuronal populations, further exploring underlying mechanisms responsible for each subflied specific functions.

Keywords: Hippocampal subfields; Hippocampus; Laser-capture microdissection; RNA-Seq; Transcriptomics.

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Conflict of interest statement

The authors declare they have no conflicts of interest.

Figures

Fig. 1
Fig. 1
Intragroup and intergroup variability (A) Barplot of the transcriptomics data displaying the number of differentially expressed transcripts identified in each hippocampal subfield comparison. (B) Venn diagram representing common and unique differentially expressed genes in all comparisons. (C) PCA graphic for hippocampal gene expression data displaying an evident cluster of samples on the different regions of the hippocampus. (D) Plotcounts of distinct marker genes for each hippocampal subfield.
Fig. 2
Fig. 2
Top significant biological processes of CA1vsCA2 and KEGG pathway of CA1vsCA3 differentially expressed genes (A) A net plot of top enriched biological processes from GO analysis of abundant CA1 genes (CA1vsCA2). (B) A dot plot of top enriched KEGG pathways of abundant CA1 genes (CA1vsCA2). All enriched pathways and biological processes displayed reached adj.p-value< .05. For the whole set of enriched biological processes and pathways, please refer to Supplementary Table 3 and 4.
Fig. 3
Fig. 3
Top significant biological processes of CA1vsCA2 and KEGG pathway of CA1vsCA3 differentially expressed genes (A) A net plot of five enriched biological processes from GO analysis of abundant CA2 genes (CA1vsCA2). (C) A dot plot of top enriched KEGG pathways of abundant CA3 genes (CA1vsCA3). All enriched pathways and biological processes displayed reached adj.p-value< .05. For the whole set of enriched biological process and pathways, please refer to Supplementary Table 3 and 4.
Fig. 4
Fig. 4
Top significant KEGG pathway of most abundant genes in DG (A) A dot plot of top enriched KEGG pathways of abundant DG genes (CA1vsDG). (B) A dot plot of top enriched KEGG pathways of abundant DG genes (CA2vsDG). (C) A dot plot of top enriched KEGG pathways of abundant DG genes (CA1vsDG). All enriched pathways and biological processes displayed reached adj.p-value< .05. For the whole set of enriched biological process and pathways, please refer to Supplementary Table 3 and 4.
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