Identification of State-Specific Proteomic and Transcriptomic Signatures of Microglia-Derived Extracellular Vesicles

Juliet V Santiago; Aditya Natu; Christina C Ramelow; Sruti Rayaprolu; Hailian Xiao; Vishnu Kumar; Prateek Kumar; Nicholas T Seyfried; Srikant Rangaraju

doi:10.1016/j.mcpro.2023.100678

Identification of State-Specific Proteomic and Transcriptomic Signatures of Microglia-Derived Extracellular Vesicles

Mol Cell Proteomics. 2023 Dec;22(12):100678. doi: 10.1016/j.mcpro.2023.100678. Epub 2023 Nov 11.

Authors

Juliet V Santiago¹, Aditya Natu¹, Christina C Ramelow¹, Sruti Rayaprolu¹, Hailian Xiao¹, Vishnu Kumar¹, Prateek Kumar¹, Nicholas T Seyfried², Srikant Rangaraju³

Affiliations

¹ Department of Neurology, Emory University, Atlanta, Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA.
² Department of Neurology, Emory University, Atlanta, Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA.
³ Department of Neurology, Emory University, Atlanta, Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA. Electronic address: srikant.rangaraju@emory.edu.

Abstract

Microglia are resident immune cells of the brain that play important roles in mediating inflammatory responses in several neurological diseases via direct and indirect mechanisms. One indirect mechanism may involve extracellular vesicle (EV) release, so that the molecular cargo transported by microglia-derived EVs can have functional effects by facilitating intercellular communication. The molecular composition of microglia-derived EVs, and how microglial activation states impact EV composition and EV-mediated effects in neuroinflammation, remain poorly understood. We hypothesize that microglia-derived EVs have unique molecular profiles that are determined by microglial activation state. Using size-exclusion chromatography to purify EVs from BV2 microglia, combined with proteomic (label-free quantitative mass spectrometry or LFQ-MS) and transcriptomic (mRNA and noncoding RNA seq) methods, we obtained comprehensive molecular profiles of microglia-derived EVs. LFQ-MS identified several classic EV proteins (tetraspanins, ESCRT machinery, and heat shock proteins), in addition to over 200 proteins not previously reported in the literature. Unique mRNA and microRNA signatures of microglia-derived EVs were also identified. After treating BV2 microglia with lipopolysaccharide (LPS), interleukin-10, or transforming growth factor beta, to mimic pro-inflammatory, anti-inflammatory, or homeostatic states, respectively, LFQ-MS and RNA seq revealed novel state-specific proteomic and transcriptomic signatures of microglia-derived EVs. Particularly, LPS treatment had the most profound impact on proteomic and transcriptomic compositions of microglia-derived EVs. Furthermore, we found that EVs derived from LPS-activated microglia were able to induce pro-inflammatory transcriptomic changes in resting responder microglia, confirming the ability of microglia-derived EVs to relay functionally relevant inflammatory signals. These comprehensive microglia-EV molecular datasets represent important resources for the neuroscience and omics communities and provide novel insights into the role of microglia-derived EVs in neuroinflammation.

Keywords: LFQ-MS; LPS; RNA sequencing; exosomes; extracellular vesicles; inflammation; microglia; proteomics; transcriptomics.

MeSH terms

Extracellular Vesicles* / metabolism
Gene Expression Profiling
Humans
Lipopolysaccharides / metabolism
Lipopolysaccharides / pharmacology
Microglia* / metabolism
Neuroinflammatory Diseases
Proteomics / methods
RNA, Messenger / genetics
RNA, Messenger / metabolism

Substances

Lipopolysaccharides
RNA, Messenger

Abstract

MeSH terms

Substances

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