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

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.

Entorhinal cortex vulnerability to human APP expression promotes hyperexcitability and tau pathology

Preventative treatment for Alzheimer's Disease is of dire importance, and yet, cellular mechanisms underlying early regional vulnerability in Alzheimer's Disease remain unknown. In human patients with Alzheimer's Disease, one of the earliest observed pathophysiological correlates to cognitive decline is hyperexcitability1. In mouse models, early hyperexcitability has been shown in the entorhinal cortex, the first cortical region impacted by Alzheimer's Disease2-4. The origin of hyperexcitability in early-stage disease and why it preferentially emerges in specific regions is unclear. Using cortical-region and cell-type- specific proteomics and patch-clamp electrophysiology, we uncovered differential susceptibility to human-specific amyloid precursor protein (hAPP) in a model of sporadic Alzheimer's. Unexpectedly, our findings reveal that early entorhinal hyperexcitability may result from intrinsic vulnerability of parvalbumin interneurons, rather than the suspected layer II excitatory neurons. This vulnerability of entorhinal PV interneurons is specific to hAPP, as it could not be recapitulated with increased murine APP expression. Furthermore, the Somatosensory Cortex showed no such vulnerability to adult-onset hAPP expression, likely resulting from PV-interneuron variability between the two regions based on physiological and proteomic evaluations. Interestingly, entorhinal hAPP-induced hyperexcitability was quelled by co-expression of human Tau at the expense of increased pathological tau species. This study suggests early disease interventions targeting non-excitatory cell types may protect regions with early vulnerability to pathological symptoms of Alzheimer's Disease and downstream cognitive decline.

Identification of state-specific proteomic and transcriptomic signatures of microglia-derived extracellular vesicles

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 impacts 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 non-coding 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 glial communities, and provide novel insights into the role of microglia-derived EVs in neuroinflammation.

Advances in proteomic phenotyping of microglia in neurodegeneration

Microglia are dynamic resident immune cells of the central nervous system (CNS) that sense, survey, and respond to changes in their environment. In disease states, microglia transform from homeostatic to diverse molecular phenotypic states that play complex and causal roles in neurologic disease pathogenesis, as evidenced by the identification of microglial genes as genetic risk factors for neurodegenerative disease. While advances in transcriptomic profiling of microglia from the CNS of humans and animal models have provided transformative insights, the transcriptome is only modestly reflective of the proteome. Proteomic profiling of microglia is therefore more likely to provide functionally and therapeutically relevant targets. In this review, we discuss molecular insights gained from transcriptomic studies of microglia in the context of Alzheimer's disease as a prototypic neurodegenerative disease, and highlight existing and emerging approaches for proteomic profiling of microglia derived from in vivo model systems and human brain.

Farnesol induces protection against CNS inflammatory demyelination and decreases spinal infiltration of CD4+ T-Cells

Multiple Sclerosis (MS) is an autoimmune disease that causes T-cells to attack and degrade the myelin sheath of neurons in the spinal cord and brain. Farnesol is synthesized by plants and mammals and has anti-inflammatory along with neuroprotective activities. We used the MOG35–55 induced c57BL/6 murine EAE (experimental autoimmune encephalomyelitis) model due to model’s neurodegenerative and inflammatory properties. We predicted that farnesol would protect against EAE and increase autoimmunity markers. We collected spinal cords and spleens for flow cytometry analysis at the end of the study. This study found that farnesol significantly reduced spinal infiltration of CD4+ T cells, and increased infiltration of Tregs compared to untreated mice. Interestingly the proportion of CD25+Foxp3+ was increased compared to untreated mice, and statistically significant compared to vehicle treatment. We did not observe significant changes in CD4+, or CD25+Foxp3+ frequencies in the spleens. FOL treatment showed significant increase in CD11b+F4/80+ monocyte-derived macrophages (MDM) and F4/80int granulocytes/monocytes. FOL also showed significant weight retention and reduction of disease severity compared to untreated. These findings show that farnesol helps mediate the invasion of CD4+ T cells in the EAE model. Future studies should study how farnesol affects T-cell activation and differentiation, along with affects on macrophages and dendritic cells.

This work was supported in part by the National Institutes of Health (grant R15NS107743)

Simultaneous RNA and protein profiling using a TurboID proximity-labeling strategy

BACKGROUND

Biologically relevant insights into cellular disease mechanisms of neurons and glia can be obtained by complimentary molecular profiling of the transcriptome and proteome of these cells. While mutually exclusive pipelines are available, the information surveyed is often from different samples leading to poor correlation between the transcriptome and proteome. Our goal was to develop a method for concomitant cell type-specific analyses of RNA and protein.

METHOD

We utilized a proximity-labeling strategy that uses the biotin ligase, TurboID, to efficiently label the proteome, in a mouse microglial BV2 cell line. We created a stable BV2-TurboID cell line that expresses TurboID fused to a nuclear export sequence. Biotin treatment of BV2-TurboID cells resulted in robust biotinylation of the cellular proteome as confirmed by Western blot and by label-free quantitation mass spectrometry (LFQ-MS) of biotinylated proteins enriched with streptavidin beads. LFQ-MS revealed that TurboID biotinylates several RNA-binding proteins (RBPs) including ribosomal units, suggesting that transcripts associated with RBPs may also be pulled down simultaneously with proteins. To test this, we homogenized BV2-Turbo and control BV2 cells, enriched biotinylated proteins with streptavidin beads while maintaining RNA-protein interactions, and then eluted RNA.

RESULT

Quality control studies showed negligible mRNA from streptavidin pulldowns from control BV2 cells, while BV2-TurboID pulldowns had larger mRNA yields with high quality. NanoString neuroinflammatory profiling (800 genes) of whole cell RNA from control BV2 and BV2-TurboID cells and streptavidin pulldowns from both cell types were performed. We observed a 23-fold higher mRNA yield in the BV2-TurboID pulldowns compared to control BV2 cells for 550 genes included in the analyses. Transcript abundances from total RNA and BV2-TurboID pulldowns were highly comparable (R² =0.97; no differentially expressed genes) with equivalent abundance of microglial genes (e.g., Spp1 and Apoe) suggesting a faithful transcriptome capture.

CONCLUSION

Our novel TurboID proximity labeling approach can simultaneously capture cell type-specific transcriptomes and proteomes. We are now validating this method in other cell types using RNA-sequencing and MS approaches. Once validated, this concurrent RNA and protein profiling approach can be applied to in vivo and ex vivo model systems to investigate the distinct roles brain cell types play in development, aging, and disease.

A Gut Feeling: The Importance of the Intestinal Microbiota in Psychiatric Disorders

The intestinal microbiota constitutes a complex ecosystem in constant reciprocal interactions with the immune, neuroendocrine, and neural systems of the host. Recent molecular technological advances allow for the exploration of this living organ and better facilitates our understanding of the biological importance of intestinal microbes in health and disease. Clinical and experimental studies demonstrate that intestinal microbes may be intimately involved in the progression of diseases of the central nervous system (CNS), including those of affective and psychiatric nature. Gut microbes regulate neuroinflammatory processes, play a role in balancing the concentrations of neurotransmitters and could provide beneficial effects against neurodegeneration. In this review, we explore some of these reciprocal interactions between gut microbes and the CNS during experimental disease and suggest that therapeutic approaches impacting the gut-brain axis may represent the next avenue for the treatment of psychiatric disorders.

Farnesol reduces T cell infiltration in murine CNS inflammatory demyelination

Farnesol (FOL) is a naturally-produced 15-carbon organic acyclic sesquiterpene alcohol (isoprenol) that acts as a potent blocker of neuronal voltage-gated Ca2+ channels (L- and N-type) and is found in the human brain. FOL has potent anti-oxidant and anti-inflammatory effects in vitro and is neuroprotective in a murine model of neurotoxicity. Because inflammation and neurodegeneration are mechanisms associated with CNS demyelinating diseases, we sought to determine whether FOL treatment would result in protection against experimental autoimmune encephalomyelitis (EAE). We compared the progression of EAE in MOG35–55 immunized female C57BL/6 mice treated orally with FOL (100 mg/kg/daily) emulsified in corn oil, versus vehicle-treated and untreated EAE mice. FOL significantly reduced the average clinical scores of EAE mice when compared to untreated mice and vehicle-treated mice. The protective effect was associated with a significant reduction of CD4+ T cell spinal cord infiltration in FOL-treated mice as assessed by flow cytometry. Although FOL’s mechanism of action remains to be known, we propose that FOL promotes protection against CNS inflammatory demyelination by promoting an anti-inflammatory effect. We compared pro-inflammatory and anti-inflammatory cytokine transcriptional levels in brain tissues of EAE mice and histological analysis of CD4+ T cell CNS infiltration and demyelination. The potential benefit of FOL nanoencapsulation in neuroprotection was explored. We demonstrate that there is a correlation between the reduced neuroinflammation and EAE severity observed in the context of FOL protection. Understanding the neuroprotective effects of FOL may provide insight to novel therapeutic approaches for MS.

Organic compound farnesol as possible inhibitor of inflammasome complex, in murine macrophages and mouse model of multiple sclerosis

Many advancements in the understanding of multiple sclerosis (MS) have been made through the use of laboratory models. One commonly used model is experimental autoimmune encephalomyelitis (EAE), a mouse model characterized by central nervous system (CNS) inflammation and demyelination, allowing for symptoms resembling some of the most prominent features of the human disease. Although the exact etiology of MS is still being investigated, experiments with EAE have shown that the NLRP3 inflammasome complex of the innate immune system is critical and necessary for disease development. The inflammasome complex can be assembled in all innate immune cells, including microglia and astrocytes in the CNS. Dysregulation of inflammasome activity can result in uncontrolled inflammation, which underlies many chronic diseases, and metabolic and autoimmune disorders such as MS. Our lab has shown that farnesol a 15-carbon organic sesquiterpene and primary alcohol, reduced EAE disease severity and onset and also decreased T-cell infiltration into the CNS. However, the mechanisms of its action have yet to be fully defined. Therefore, in-vitro work on murine macrophages is being conducted to investigate how farnesol may be potentially affecting the pathway of the inflammasome complex and providing this protection. Furthermore, since farnesol is a quorum-sensing molecule that impacts biofilm formation, other studies of ours are aimed at evaluating how farnesol affects the gut-brain axis and specifically the gut microbiome of EAE mice.