Quantitative Proteomics Reveals Temporal Proteomic Changes in Signaling Pathways during BV2 Mouse Microglial Cell Activation

The immunometabolic reprogramming of microglia in Alzheimer's disease

Alzheimer's disease (AD) is an age-related neurodegenerative disorder (NDD). In the central nervous system (CNS), immune cells like microglia could reprogram intracellular metabolism to alter or exert cellular immune functions in response to environmental stimuli. In AD, microglia could be activated and differentiated into pro-inflammatory or anti-inflammatory phenotypes, and these differences in cellular phenotypes resulted in variance in cellular energy metabolism. Considering the enormous energy requirement of microglia for immune functions, the changes in mitochondria-centered energy metabolism and substrates of microglia are crucial for the cellular regulation of immune responses. Here we reviewed the mechanisms of microglial metabolic reprogramming by analyzing their flexible metabolic patterns and changes that occurred in their metabolism during the development of AD. Further, we summarized the role of drugs in modulating immunometabolic reprogramming to prevent neuroinflammation, which may shed light on a new research direction for AD treatment.

Extracellular histones as damage-associated molecular patterns in neuroinflammatory responses

The four core histones H2A, H2B, H3, H4, and the linker histone H1 primarily bind DNA and regulate gene expression within the nucleus. Evidence collected mainly from the peripheral tissues illustrates that histones can be released into the extracellular space by activated or damaged cells. In this article, we first summarize the innate immune-modulatory properties of extracellular histones and histone-containing complexes, such as nucleosomes, and neutrophil extracellular traps (NETs), described in peripheral tissues. There, histones act as damage-associated molecular patterns (DAMPs), which are a class of endogenous molecules that trigger immune responses by interacting directly with the cellular membranes and activating pattern recognition receptors (PRRs), such as toll-like receptors (TLR) 2, 4, 9 and the receptor for advanced glycation end-products (RAGE). We then focus on the available evidence implicating extracellular histones as DAMPs of the central nervous system (CNS). It is becoming evident that histones are present in the brain parenchyma after crossing the blood-brain barrier (BBB) or being released by several types of brain cells, including neurons, microglia, and astrocytes. However, studies on the DAMP-like effects of histones on CNS cells are limited. For example, TLR4 is the only known molecular target of CNS extracellular histones and their interactions with other PRRs expressed by brain cells have not been observed. Nevertheless, extracellular histones are implicated in the pathogenesis of a variety of neurological disorders characterized by sterile neuroinflammation; therefore, detailed studies on the role these proteins and their complexes play in these pathologies could identify novel therapeutic targets.

Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines

Different brain cell types play distinct roles in brain development and disease. Molecular characterization of cell-specific mechanisms using cell type-specific approaches at the protein (proteomic) level can provide biological and therapeutic insights. To overcome the barriers of conventional isolation-based methods for cell type-specific proteomics, in vivo proteomic labeling with proximity-dependent biotinylation of cytosolic proteins using biotin ligase TurboID, coupled with mass spectrometry (MS) of labeled proteins, emerged as a powerful strategy for cell type-specific proteomics in the native state of cells without the need for cellular isolation. To complement in vivo proximity labeling approaches, in vitro studies are needed to ensure that cellular proteomes using the TurboID approach are representative of the whole-cell proteome and capture cellular responses to stimuli without disruption of cellular processes. To address this, we generated murine neuroblastoma (N2A) and microglial (BV2) lines stably expressing cytosolic TurboID to biotinylate the cellular proteome for downstream purification and analysis using MS. TurboID-mediated biotinylation captured 59% of BV2 and 65% of N2A proteomes under homeostatic conditions. TurboID labeled endolysosome, translation, vesicle, and signaling proteins in BV2 microglia and synaptic, neuron projection, and microtubule proteins in N2A neurons. TurboID expression and biotinylation minimally impacted homeostatic cellular proteomes of BV2 and N2A cells and did not affect lipopolysaccharide-mediated cytokine production or resting cellular respiration in BV2 cells. MS analysis of the microglial biotin-labeled proteins captured the impact of lipopolysaccharide treatment (>500 differentially abundant proteins) including increased canonical proinflammatory proteins (Il1a, Irg1, and Oasl1) and decreased anti-inflammatory proteins (Arg1 and Mgl2).

Microglia secrete distinct sets of neurotoxins in a stimulus-dependent manner

Microglia are the resident immune cells of the brain which regulate both the innate and adaptive neuroimmune responses in health and disease. In response to specific endogenous and exogenous stimuli, microglia transition to one of their reactive states characterized by altered morphology and function, including their secretory profile. A component of the microglial secretome is cytotoxic molecules capable of causing damage and death to nearby host cells, thus contributing to the pathogenesis of neurodegenerative disorders. Indirect evidence from secretome studies and measurements of mRNA expression using diverse microglial cell types suggest different stimuli may induce microglia to secrete distinct subsets of cytotoxins. We demonstrate the accuracy of this hypothesis directly by challenging murine BV-2 microglia-like cells with eight different immune stimuli and assessing secretion of four potentially cytotoxic molecules, including nitric oxide (NO), tumor necrosis factor α (TNF), C-X-C motif chemokine ligand 10 (CXCL10), and glutamate. Lipopolysaccharide (LPS) and a combination of interferon (IFN)-γ plus LPS induced secretion of all toxins studied. IFN-β, IFN-γ, polyinosinic:polycytidylic acid (poly I:C), and zymosan A upregulated secretion of subsets of these four cytotoxins. LPS and IFN-γ, alone or in combination, as well as IFN-β induced toxicity of BV-2 cells towards murine NSC-34 neuronal cells, while ATP, N-formylmethionine-leucyl-phenylalanine (fMLP), and phorbol 12-myristate 13-acetate (PMA) did not affect any parameters studied. Our observations contribute to a growing body of knowledge on the regulation of the microglial secretome, which may inform future development of novel therapeutics for neurodegenerative diseases, where dysregulated microglia are key contributors to pathogenesis.

Cardiolipin released by microglia can act on neighboring glial cells to facilitate the uptake of amyloid-β (1-42)

Cardiolipin is a mitochondrial phospholipid that is also detected in serum inferring its extracellular release; however, this process has not been directly demonstrated for any of the brain cell types. Nevertheless, extracellular cardiolipin has been shown to modulate several neuroimmune functions of microglia and astrocytes, including upregulation of their endocytic activity. Low cardiolipin levels are associated with brain aging, and may thus hinder uptake of amyloid-β (Αβ) in Alzheimer's disease. We hypothesized that glial cells are one of the sources of extracellular cardiolipin in the brain parenchyma where this phospholipid interacts with neighboring cells to upregulate the endocytosis of Αβ. Liquid chromatography-mass spectrophotometry identified 31 different species of cardiolipin released from murine BV-2 microglial cells and revealed this process was accelerated by exposure to Aβ42. Extracellular cardiolipin upregulated internalization of fluorescently-labeled Aβ42 by primary murine astrocytes, human U118 MG astrocytic cells, and murine BV-2 microglia. Increased endocytic activity in the presence of extracellular cardiolipin was also demonstrated by studying uptake of Aβ42 and pHrodo™ Bioparticles™ by human induced pluripotent stem cells (iPSCs)-derived microglia, as well as iPSC-derived human brain organoids containing microglia, astrocytes, oligodendrocytes and neurons. Our observations indicate that Aβ42 augments the release of cardiolipin from microglia into the extracellular space, where it can act on microglia and astrocytes to enhance their endocytosis of Aβ42. Our observations suggest that the reduced glial uptake of Aβ due to the decreased levels of cardiolipin could be at least partially responsible for the extracellular accumulation of Aβ in aging and Alzheimer's disease.

Microglia modulate proliferation, neurite generation and differentiation of human neural progenitor cells

Microglia, the primary immune cells of the brain, significantly influence the fate of neurons after neural damage. Depending on the local environment, they exhibit a wide range of phenotypes, including patrolling (naïve), proinflammatory, and anti-inflammatory characteristics, which greatly affects neurotoxicity. Despite the fact that neural progenitor cells (NPCs) and hippocampal neurons represent cell populations, which play pivotal role in neural regeneration, interaction between microglia and these cell types is poorly studied. In the present work, we investigated how microglial cells affect the proliferation and neurite outgrowth of human stem cell-derived NPCs, and how microglia stimulation with proinflammatory or anti-inflammatory agents modulates this interaction. We found that naïve microglia slightly diminish NPC proliferation and have no effect on neurite outgrowth. In contrast, proinflammatory stimulated microglia promote both proliferation and neurite generation, whereas microglia stimulated with anti-inflammatory cytokines augment neurite outgrowth leaving NPC proliferation unaffected. We also studied how microglia influence neurite development and differentiation of hippocampal dentate gyrus granule cells differentiated from NPCs. We found that proinflammatory stimulated microglia inhibit axonal development but facilitate dendrite generation in these differentiating neurons. Our results elucidate a fine-tuned modulatory effect of microglial cells on cell types crucial for neural regeneration, opening perspectives for novel regenerative therapeutic interventions.

Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives

Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.

Potential neurotoxic activity of diverse molecules released by microglia

Microglia are the professional immune cells of the brain, which support numerous physiological processes. One of the defensive functions provided by microglia involves secretion of cytotoxins aimed at destroying invading pathogens. It is also recognized that the adverse activation of microglia in diseased brains may lead to secretion of cytotoxic molecules, which could be damaging to the surrounding cells, including neurons. Several of these toxins, such as reactive oxygen and nitrogen species, L-glutamate, and quinolinic acid, are widely recognized and well-studied. This review is focused on a structurally diverse group of less-established microglia neurotoxins, which were selected by applying the two criteria that these molecules 1) can be released by microglia, and 2) have the potential to be directly harmful to neurons. The following 11 molecules are discussed in detail: amyloid beta peptides (Aβ); cathepsin (Cat)B and CatD; C-X-C motif chemokine ligand (CXCL)10 and CXCL12 (5-67); high mobility group box (HMGB)1; lymphotoxin (LT)-α; matrix metalloproteinase (MMP)-2 and MMP-9; platelet-activating factor (PAF); and prolyl endopeptidase (PEP). Molecular mechanisms of their release by microglia and neurotoxicity, as well as available evidence implicating their involvement in human neuropathologies are summarized. Further studies on several of the above molecules are warranted to confirm either their microglial origin in the brain or direct neurotoxic effects. In addition, investigations into the differential secretion patterns of neurotoxins by microglia in response to diverse stimuli are required. This research could identify novel therapeutic targets for neurological disorders involving adverse microglial activation.

Tween 20 regulate the function and structure of transmembrane proteins of Bacillus cereus: Promoting transmembrane transport of fluoranthene

Polycyclic aromatic hydrocarbons (PAHs) are degraded by the highly efficient degrading bacterium Bacillus cereus. Transmembrane transport is highly important in PAH degradation by bacteria. Surfactants are the key substances that promote PAH adsorption, uptake and transmembrane transport by Bacillus cereus. In this study, the isobaric tags for relative and absolute quantitation (iTRAQ) approach was used for high-throughput screening of key functional proteins during transmembrane fluoranthene transport by Bacillus cereus treated with Tween 20. In addition, SWISS-MODEL was used to simulate the tertiary structures of key transmembrane proteins and analyze how Tween 20 promotes transmembrane transport. Transmembrane fluoranthene transport into Bacillus cereus requires transmembrane proteins and energy. Tween 20 was observed to improve bacterial motility and transmembrane protein expression. The interior of representative transmembrane proteins is mostly composed of hydrophobic β-sheets while amphipathic α-helices are primarily distributed at their periphery. The primary reason for this configuration may be α-helices promote the aggregation of surfactants and the phospholipid bilayer and the β-sheets promote surfactant insertion into the phospholipid bilayer to enhance PAH transport into Bacillus cereus. Investigating the effect of Tween 20 on Bacillus cereus transmembrane proteins during transmembrane fluoranthene transport is important for understanding the mechanism of PAH degradation by microorganisms.

Quantitative proteomics approach to investigate the antibacterial response of Helicobacter pylori to daphnetin, a traditional Chinese medicine monomer

Helicobacter pylori is a Gram-negative bacterium related to the development of peptic ulcers and stomach cancer. An increasing number of infected individuals are found to harbor antibiotic-resistant H. pylori, which results in treatment failure. Daphnetin, a traditional Chinese medicine, has a broad spectrum of antibacterial activity without the development of bacterial resistance. However, the antibacterial mechanisms of daphnetin have not been elucidated entirely. To better understand the mechanisms of daphnetin's effect on H. pylori, a label-free quantitative proteomics approach based on an EASY-nLC 1200 system coupled with an Orbitrap Fusion Lumos mass spectrometer was established to investigate the key protein differences between daphnetin- and non-daphnetin-treated H. pylori. Using the criteria of greater than 1.5-fold changes and adjusted p value <0.05, proteins related to metabolism, membrane structure, nucleic acid and protein synthesis, ion binding, H. pylori colonization and infection, stress reaction, flagellar assembly and so on were found to be changed under daphnetin pressure. And the changes of selected proteins in expression level were confirmed by targeted proteomics. These new data provide us a more comprehensive horizon of the proteome changes in H. pylori that occur in response to daphnetin.

Quantitative Proteomics Reveals Docosahexaenoic Acid-Mediated Neuroprotective Effects in Lipopolysaccharide-Stimulated Microglial Cells

The high levels of docosahexaenoic acid (DHA) in cell membranes within the brain have led to a number of studies exploring its function. These studies have shown that DHA can reduce inflammatory responses in microglial cells. However, the method of action is poorly understood. Here, we report the effects of DHA on microglial cells stimulated with lipopolysaccharides (LPSs). Data were acquired using the parallel accumulation serial fragmentation method in a hybrid trapped ion mobility-quadrupole time-of-flight mass spectrometer. Over 2800 proteins are identified using label-free quantitative proteomics. Cells exposed to LPSs and/or DHA resulted in changes in cell morphology and expression of 49 proteins with differential abundance (greater than 1.5-fold change). The data provide details about pathways that are influenced in this system including the nuclear factor κ-light-chain-enhancer of the activated B cells (NF-κB) pathway. Western blots and enzyme-linked immunosorbent assay studies are used to help confirm the proteomic results. The MS data are available at ProteomeXchange.

Al-induced proteomics changes in tomato plants over-expressing a glyoxalase I gene

Glyoxalase I (Gly I) is the first enzyme in the glutathionine-dependent glyoxalase pathway for detoxification of methylglyoxal (MG) under stress conditions. Transgenic tomato 'Money Maker' plants overexpressing tomato SlGlyI gene (tomato unigene accession SGN-U582631/Solyc09g082120.3.1) were generated and homozygous lines were obtained after four generations of self-pollination. In this study, SlGlyI-overepxressing line (GlyI), wild type (WT, negative control) and plants transformed with empty vector (ECtr, positive control), were subjected to Al-treatment by growing in Magnavaca's nutrient solution (pH 4.5) supplemented with 20 µM Al3+ ion activity. After 30 days of treatments, the fresh and dry weight of shoots and roots of plants from Al-treated conditions decreased significantly compared to the non-treated conditions for all the three lines. When compared across the three lines, root fresh and dry weight of GlyI was significant higher than WT and ECtr, whereas there was no difference in shoot tissues. The basal 5 mm root-tips of GlyI plants expressed a significantly higher level of glyoxalase activity under both non-Al-treated and Al-treated conditions compared to the two control lines. Under Al-treated condition, there was a significant increase in MG content in ECtr and WT lines, but not in GlyI line. Quantitative proteomics analysis using tandem mass tags mass spectrometry identified 4080 quantifiable proteins and 201 Al-induced differentially expressed proteins (DEPs) in root-tip tissues from GlyI, and 4273 proteins and 230 DEPs from ECtr. The Al-down-regulated DEPs were classified into molecular pathways of gene transcription, RNA splicing and protein biosynthesis in both GlyI and ECtr lines. The Al-induced DEPs in GlyI associated with tolerance to Al3+ and MG toxicity are involved in callose degradation, cell wall components (xylan acetylation and pectin degradation), oxidative stress (antioxidants) and turnover of Al-damaged epidermal cells, repair of damaged DNA, epigenetics, gene transcription, and protein translation. A protein-protein association network was constructed to aid the selection of proteins in the same pathway but differentially regulated in GlyI or ECtr lines. Proteomics data are available via ProteomeXchange with identifiers PXD009456 under project title '25Dec2017_Suping_XSexp2_ITAG3.2' for SlGlyI-overexpressing tomato plants and PXD009848 under project title '25Dec2017_Suping_XSexp3_ITAG3.2' for positive control ECtr line transformed with empty vector.

Quantitative Proteomics Reveals Distinct Molecular Signatures of Different Cerebellum-Dependent Learning Paradigms

The cerebellum improves motor performance by adjusting motor gain appropriately. As de novo protein synthesis is essential for the formation and retention of memories, we hypothesized that motor learning in the opposite direction would induce a distinct pattern of protein expression in the cerebellum. We conducted quantitative proteomic profiling to compare the level of protein expression in the cerebellum at 1 and 24 h after training from mice that underwent different paradigms of cerebellum-dependent oculomotor learning from specific directional changes in motor gain. We quantified a total of 43 proteins that were significantly regulated in each of the three learning paradigms in the cerebellum at 1 and 24 h after learning. In addition, functional enrichment analysis identified protein groups that were differentially enriched or depleted in the cerebellum at 24 h after the three oculomotor learnings, suggesting that distinct biological pathways may be engaged in the formation of three oculomotor memories. Weighted correlation network analysis discovered groups of proteins significantly correlated with oculomotor memory. Finally, four proteins (Snca, Sncb, Cttn, and Stmn1) from the protein group correlated with the learning amount after oculomotor training were validated by Western blot. This study provides a comprehensive and unbiased list of proteins related to three cerebellum-dependent motor learning paradigms, suggesting the distinct nature of protein expression in the cerebellum for each learning paradigm. The proteomics data have been deposited to the ProteomeXchange Consortium with identifiers <PXD008433>.

Deep proteome profiling of the hippocampus in the 5XFAD mouse model reveals biological process alterations and a novel biomarker of Alzheimer's disease

Alzheimer’s disease (AD), which is the most common type of dementia, is characterized by the deposition of extracellular amyloid plaques. To understand the pathophysiology of the AD brain, the assessment of global proteomic dynamics is required. Since the hippocampus is a major region affected in the AD brain, we performed hippocampal analysis and identified proteins that are differentially expressed between wild-type and 5XFAD model mice via LC-MS methods. To reveal the relationship between proteomic changes and the progression of amyloid plaque deposition in the hippocampus, we analyzed the hippocampal proteome at two ages (5 and 10 months). We identified 9,313 total proteins and 1411 differentially expressed proteins (DEPs) in 5- and 10-month-old wild-type and 5XFAD mice. We designated a group of proteins showing the same pattern of changes as amyloid beta (Aβ) as the Aβ-responsive proteome. In addition, we examined potential biomarkers by investigating secretory proteins from the Aβ-responsive proteome. Consequently, we identified vitamin K-dependent protein S (PROS1) as a novel microglia-derived biomarker candidate in the hippocampus of 5XFAD mice. Moreover, we confirmed that the PROS1 level in the serum of 5XFAD mice increases as the disease progresses. An increase in PROS1 is also observed in the sera of AD patients and shows a close correlation with AD neuroimaging markers in humans. Therefore, our quantitative proteome data obtained from 5XFAD model mice successfully predicted AD-related biological alterations and suggested a novel protein biomarker for AD.

A protein newly implicated in Alzheimer’s disease could serve as a diagnostic biomarker or therapeutic target. A team led by Youngsoo Kim and Inhee Mook-Jung from Seoul National University, South Korea, analyzed all the proteins expressed in the hippocampus, the brain’s memory center, in mice with and without Alzheimer’s-like disease. They identified more than 1,400 proteins differentially expressed between the mouse model of Alzheimer’s and the normal mice. Among these were 36 secretory proteins that tended to increase their levels along with build-up of amyloid-beta, the protein found in clumps in the brains of people with Alzheimer’s. Many already had known links to Alzheimer’s, but the researchers also identified a novel protein called PROS1. Blood samples from Alzheimer’s patients also showed an increase in PROS1 levels, with a close correlation with amyloid-beta build-up in the brain.

iTRAQ-based secretome reveals that SiO2 induces the polarization of RAW264.7 macrophages by activation of the NOD-RIP2-NF-κB signaling pathway

Silicosis is characterized by inflammation and pulmonary fibrosis due to long-term inhalation of crystalline silica (SiO₂). To clarify the role of macrophage polarization in the inflammatory response of silicosis, we used iTRAQ-coupled 2D LC-MS/MS to study the change in the secretome in RAW264.7 macrophages. We successfully screened 330 differentially expressed proteins, including 120 proteins with upregulated expression and 210 proteins with down-regulated expression (p < 0.05). Bioinformatics analysis showed that the differentially expressed proteins were mainly involved in biological processes, such as oxidative stress, mitochondrial damage, apoptosis and acute inflammatory response. In particular, the expression levels of mitochondrial apoptosis-related proteins, such as AKT1, BAX, HSPD1, TNF, CASP8 and DAP, were increased after SiO₂ exposure. Taken together, our study indicated that SiO₂ could induce macrophage polarization by activation of the NOD-RIP2-NF-κB signaling pathway in RAW264.7 macrophages. This may represent a potential mechanism in the development of silicosis.

Determination of Site-Specific Phosphorylation Ratios in Proteins with Targeted Mass Spectrometry

We show that parallel reaction monitoring (PRM) can be used for exact quantification of phosphorylation ratios of proteins using stable-isotope-labeled peptides. We have compared two different PRM approaches on a digest of a U87 cell culture, namely, direct-PRM (tryptic digest measured by PRM without any further sample preparation) and TiO₂-PRM (tryptic digest enriched with TiO₂ cartridges, followed by PRM measurement); these approaches are compared for the following phosphorylation sites: neuroblast differentiation-associated protein (AHNAK S5480-p), calcium/calmodulin-dependent protein kinase type II subunit delta (CAMK2D T337-p), and epidermal growth factor receptor (EGFR S1166-p). A reproducible percentage of phosphorylation could be determined (CV 6-13%) using direct-PRM or TiO₂-PRM. In addition, we tested the approaches in a cell culture experiment in which U87 cells were deprived of serum. As a "gold standard" we included immune precipitation of EGFR followed by PRM (IP-PRM). For EGFR (S1166) and AHNAK (S5480) a statistical significant change in the percentage of phosphorylation could be observed as a result of serum deprivation; for EGFR (S1166) this change was observed for both TiO₂-PRM and IP-PRM. The presented approach has the potential to multiplex and to quantify the ratio of phosphorylation in a single analysis.