Deconvolution of Human Brain Cell Type Transcriptomes Unraveled Microglia-Specific Potential Biomarkers

Frontiers in Neurology
R AyanaSoumya Pati

Abstract

Microglial cells form a context-dependent network of brain immunoeffector cells. Despite their indispensable roles, unresolved questions exist around biomarker discovery relevant to their cellular localization, self-renewing potential, and brain developmental dynamics. To resolve the existent gap in the annotation of candidate biomarkers, we conducted a meta-analysis of brain cells using available high-throughput data sets for deciphering microglia-specific expression profiles. We have identified 3,290 significant genes specific to microglia and further selected the top 20 dysregulated genes on the basis of p-value and log2FC. To this list, we added 7 known microglia-specific markers making the candidate list comprising 27 genes for further downstream analyses. Next, we established a connectome of these potential markers with their putative protein partners, which demonstrated strong associations of upregulated genes like Dedicator of cytokinesis 2 (DOCK2) with early/mature microglial markers such as Sphingosine kinase 1 (SPHK1), CD68, and CD45. To elucidate their respective brain anatomical location, we deconvoluted the BrainSpan Atlas expression data. This analysis showed high expression of the majority of candidate genes in ...Continue Reading

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Citations

Feb 11, 2021·Clinical and Experimental Immunology·J L EbersoleO A Gonzalez
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Methods Mentioned

BETA
Protein
RNA-Seq
scraping
nucleotide
GTPases
flow cytometry

Software Mentioned

OLIGO
Corrplot
STRING
Bioconductor
GSE
R
DDM
Protein ANalysis THrough Evolutionary
R Bioconductor
R Bioconductor suite

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