Work

Transcriptome characterization of the motor cortex suggests microglial‐related key events due to TDP‐43 aberrant inclusions

Year: 2020

Type: article

Abstract: Background TAR DNA binding protein 43 (TDP‐43) is an RNA binding protein with a central role in transcription regulation. Evaluation of the transcriptome in affected brain tissues with aggregated TDP‐43 will allow us to better understand the pathological processes occurring in a variety of neurodegenerative disorders. Method We performed massive RNA sequencing in the motor cortex (BA4) of amyotrophic lateral sclerosis (ALS) patients (n = 11) and controls without lesions (HC; n = 8). Differential gene and isoform expression between patients and controls were evaluated with DESeq2. Gene ontology and KEGG pathway enrichment analyses were applied using default parameters in Metascape 3.0. The Multi‐Subject Single Cell deconvolution algorithm (MuSiC) was used to perform cell‐type deconvolution of our bulk RNAseq data. Formalin‐fixed and paraffin‐embedded motor cortex sections were used for immunohistochemistry, with IBA1 and ps409/410‐TDP primary antibodies. For immunofluorescence, anti‐MHCII markers (HLA‐DP,DQ,DR) and anti‐IBA1 were employed. Result Differential gene expression between ALS patients and HC disclosed 108 up‐regulated and 16 down‐regulated genes in the motor cortex (Figure 1; adj. p < 0,05). Gene ontology and KEGG pathway analyses revealed an enriched involvement of the inflammatory response in ALS. The assessment of changes at the isoform expression level also pointed towards an enrichment of the immune response as a dominant pathway, but also revealed a postsynaptic involvement. Characterization of cell type variability from bulk RNA‐seq data, using available single‐nucleus RNAseq data comprising 70.634 cells from Alzheimer’s disease and HC subjects (n = 48) (Mathys et al., Nature 2019) as reference, revealed an overrepresentation of microglial cells in the ALS motor cortex as compared to HC (p = 0,025) (Figure 2). Our deconvolution analysis also showed that a specific microglial subpopulation, recognized as the recently described disease associated microglia (DAM) was disproportionately present in ALS (p = 6,6 × 10−3) (Figure 3). Immunofluorescence through the combination of IBA1 and MHC class II markers confirmed the over representation of this cell subtype in the motor area of ALS cases. Conclusion The presence of insoluble TDP‐43 inclusions in affected brain tissue leads to RNA dyshomeostasis, with genes related to inflammation and synaptic functions as major altered transcriptome signatures. The recently described DAM play a key role in ALS and maybe other TDP‐43 related proteinopathies.

Source: Alzheimer s & Dementia

DOI: 10.1002/alz.042953