Differentially expressed genes in different brain regions with a focus on the matrisome

Abstract

The project aims to investigate the expression of the matrisome, composed of components of the extracellular matrix, in eight different human brain sites from autopsies. Preliminary analysis involved examining variations in the expression of genes encoding core matrisome proteins in tissues from the cerebellum (9), hippocampus (HCP; 8), hypothalamus (7), substantia nigra (5), and isocortex (34) - including those from the temporal (5), occipital (5), frontal (8), and parietal (16) lobes - using transcriptome data (RNA-Seq) available in the research group. Comparative analysis focused on HCP, given its involvement in prevalent neurodegenerative diseases such as Alzheimer's and Parkinson's, in relation to other sites. A total of 95 differentially expressed genes (DEGs) were identified in HCP compared to other sites, including 19 collagen-encoding genes, 64 glycoprotein-encoding genes, and 12 proteoglycan-encoding genes (p<0.05, Kruskal-Wallis test). The selection of the DEG with the highest statistical significance among those with the greatest expression difference [log fold change (FC)] was performed among the glycoprotein-encoding genes, as these proteins are subject to post-transcriptional modifications and are therefore more susceptible to differential modulation between homeostatic and disease conditions. Two members of the SLIT (slit guidance ligand) family, SLIT2 and SLIT3, showed significant differences in HCP compared to other brain sites (p<0.0005, Kruskal-Wallis test) and had significant adjusted p-values when comparing expression in HCP with expression in other sites (p<0.0005, Limma test, pairwise comparison). SLIT family proteins are key regulators in guiding axonal migration and neural precursor cells, preventing abnormal midline crossing during embryonic nervous system development. They act as axon repellents, guiding them in specific directions through interaction with their receptors, called Roundabout proteins (ROBO). The SLIT-ROBO signaling is involved in various biological processes, including axonal guidance, organogenesis, angiogenesis, vascular development, endothelial migration, leukocyte chemotaxis, and tumor metastasis.In the second stage of the project, the proposal is to validate the gene expression of SLIT family members (SLIT1-3) and their cognate ROBO family receptors (ROBO1-4) using real-time quantitative PCR in samples of brain tissue from different sites in an independent and expanded series. Targets whose differential gene expression is confirmed in HCP will be assessed at the protein level through immunohistochemistry and western blot.The aim is to confirm the differential expression of selected targets in HCP under homeostatic conditions to enable comparison under disease conditions, such as neurodegenerative diseases, traumatic brain injury, and tumors of the central nervous system.