Method Article
A protocol was developed for the preparation of purified mitochondria from microglial cells, isolation of mitochondrial proteins for N-glycan release, and rapid detection of subcellular, mitochondrial glycans using infrared matrix-assisted laser desorption electrospray ionization coupled to high-resolution accurate mass analyzer mass spectrometry.
Understanding the glycosylation patterns of mitochondrial proteins in microglia is critical for determining their role in neurodegenerative diseases. Here, we present a novel and high-throughput methodology for glycomic analysis of mitochondrial proteins isolated from cultured microglia. This method involves the isolation of mitochondria from microglial cultures, quality assessment of mitochondrial samples, followed by an optimized protein extraction to maximize glycan detection, and infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) high-resolution accurate mass (HRAM) mass spectrometry to provide detailed profiles of mitochondrial glycosylation.
This protocol emphasizes the importance of maintaining mitochondrial integrity during isolation and employs stringent quality control to ensure reproducibility, including measuring mitochondrial purity after extraction. This approach allows for the comprehensive profiling of glycosylation changes in microglial mitochondria under various experimental conditions in vitro, which offers insight into mitochondrial changes associated with neurodegenerative diseases. This approach could be adapted to other in vitro treatments, other cultured cell types, or primary cells. Through this standardized approach, we aim to advance the understanding of microglial mitochondrial glycans, contributing to the broader field of neurodegenerative research.
Microglia are the dominant resident innate immune cells in the brain and account for 10-15% of cells in the adult brain1,2. They use their receptor repertoire to dynamically monitor the brain microenvironment and regulate the normal brain function to maintain brain homeostasis3. Microglia are very sensitive to the changes in their microenvironment and undergo changes in cell morphology, immunophenotype, and function with pathological conditions or various stimulations. Microglial activation states are influenced by the cellular energy demands required for their function, such as phagocytosis, cytokine production, or tissue repair. Therefore, cellular energy metabolism plays a crucial role in regulating changes in microglial function4. Microglial dysregulation leads to excessive release of pro-inflammatory cytokines (e.g., IL-1β, TNF-α) and reactive oxygen species (ROS), predisposing the brain to neuroinflammation5,6. Chronic microglial dysregulation and the resulting neuroinflammatory environment lays a foundation for neurodegeneration7.
The brain accounts for only 2% of body weight but 20% of the body's total energy consumption. Mitochondria are the primary source of energy in brain cells and act as key players in the pathogenesis of both acute and chronic brain disorders8. Previous studies have established a strong correlation between microglial activation and metabolic dysfunction in aging9 and age-related disorders such as Alzheimer's disease10,11, highlighting the pivotal role of mitochondria in cellular senescence and neurodegeneration. Impaired mitochondrial function leads to diminished energy production, elevated oxidative stress, and increased neuroinflammation during aging and age-related diseases.
While extensive research has elucidated the role of mitochondria in energy metabolism, aging, and brain disorders, the role of common post-translational modifications, such as glycosylation, in mitochondrial biology and function remains insufficiently explored. Glycosylation, the enzymatic addition of sugar moieties called glycans to proteins by glycosylation enzymes, is the most common post-translational modification in most brain cells, including microglia. Activated microglia modulate their immune function under inflammatory stimuli by regulating the intracellular or cell surface glycan expression12. The pro- and anti-inflammatory responses exhibited by microglia post-stimulation are also regulated by the glycans13. Mitochondrial proteins also have these glycan modifications, which regulate their function and localization. However, detailed analysis of the cell-specific mitochondrial glycosylation patterns in the microglia is lacking due to the technical challenges in investigating sub-cellular glycosylation. Despite the well-characterized roles of glycosylation in modulating the microglial phenotype, the role of glycans in modulating mitochondrial function and subsequently, cellular immunophenotype in microglia remains poorly understood.
Limited studies investigating mitochondrial protein glycosylation have focused primarily on lectin-based identification of glycosylation patterns. Lectins are glycan-binding proteins that bind biomolecular glycan moieties14,15, which lack the specificity and ability to provide detailed information about the glycan composition. Mass spectrometric modalities offer a detailed identification of the glycan compositions to overcome the analytical challenges presented by lectin analysis. One such modality, infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI), employs a hybrid ionization strategy, using a mid-IR laser to resonantly excite water found in biological specimens16 to desorb the neutral species and subject them to an orthogonal electrospray plume, followed by analysis using a high-resolution accurate mass Orbitrap mass spectrometer. IR-MALDESI has been previously demonstrated for the direct analysis of tissue metabolites17, with distinct advantages of rapid analysis18, soft ionization method, and the predictability of sialic acid content of N-linked glycans based on the isotopic distribution patterns of chlorinated glycan adducts19. However, the adaptation of this platform for the direct analysis of sub-cellular glycans has not been demonstrated.
Here, we report a high-throughput protocol for mitochondrial isolation from microglial cells, isolation of mitochondrial N-glycans, and mitochondrial N-glycan detection and analysis using IR-MALDESI mass spectrometry. This protocol will be foundational in uncovering novel insights into the role of glycosylation in mitochondrial function, potentially identifying new therapeutic targets for neuroinflammatory and neurodegenerative disorders.
1. BV2 Microglial cell line culture
2. Isolation of mitochondria from microglial cells
NOTE: Work quickly, keeping everything on ice throughout the procedure. The mitochondrial isolation kit used for mitochondrial isolation has three components: Reagents A (cell lysis buffer), Reagent B (stabilizing buffer), and Reagent C (mitochondrial wash buffer). Add protease inhibitors to reagent A and reagent C immediately before use.
3. Protein estimation using microBCA assay
NOTE: Protein estimation for this protocol can be performed using different reagents and assays. Quantification of cytosolic or mitochondrial proteins can be performed by normalizing against the total protein concentration used in the assay.
4. Mitochondrial preparation quality control (western blot)
5. Mitochondrial protein isolation for N -glycan extraction from microglia
6. Mitochondrial N -glycan preparation for IR-MALDESI
7. Detection of released glycans by IR-MALDESI mass spectrometry
8. Mitochondrial N- glycan data analysis
Figure 1 represents a schematic outline of the steps involved in the isolation of mitochondria from the BV2 microglial cell line for mass spectrometric glycan analysis. The reproducibility of mitochondrial protein isolation between different mitochondrial preparations from the same starting density of the microglial cells is represented in Figure 2, which shows no significant difference between the mitochondrial protein concentration estimated using the micro BCA assay.
Figure 3 represents the purity of mitochondrial isolations using western blot analysis of COX IV and GAPDH. Here, we see the expression of the mitochondrial protein COX IV in the mitochondrial fraction isolated in the final step of the reagent-based isolation used in the protocol. The immunoblots show a prominent COX IV band in the isolated mitochondrial fraction, while GAPDH is only detected in the cytoplasmic fraction at the same exposure. Longer exposure times can result in the detection of a faint GAPDH band. Expression of the non-mitochondrial marker GAPDH is evident in the whole cell lysate after isolation of mitochondria, without the CoxIV bands, indicating a complete isolation of the mitochondrial fraction and minimal non-mitochondrial contamination. COX IV expression in the mitochondrial fractions is consistent between different preparations with similar starting cell density of 2 × 107 cells.
Representative mass spectra of the released N-glycans detected using IR-MALDESI in Figure 4 shows the presence of several phosphorylated, sulfated, and sialylated charged N-glycans released from the mitochondrial protein extract using PNGase treatment. Table 2 reports all the glycan compositions that were identified in the whole spectra but were not reported in GlyConnect. Chi-squared values testing a goodness-of-fit confirm the detection of N-linked glycans with one and two chlorine adducts, confirming the detection of these glycan compositions using IR-MALDESI in Figure 5.
Figure 1: Protocol outline. Schematic outline of the mitochondrial isolation, quality control, protein extraction, N-glycan release, and estimation using IR-MALDESI HRAM mass spectrometry from BV2 microglial cell line for high throughput detection of mitochondrial N-glycans. Abbreviation: IR-MALDESI HRAM = Infrared-Matrix-Assisted Laser Desorption Electrospray Ionization High-Resolution Accurate Mass Analyzer. Please click here to view a larger version of this figure.
Figure 2: Mitochondrial protein isolation from BV2 cells. (A) Standard curve for micro BCA assay using different concentrations of BSA. (B) Reproducibility of the mitochondrial protein isolation represented by consistent protein content from 2 × 107 cells in six independent mitochondrial preparations. Please click here to view a larger version of this figure.
Figure 3: Purity of mitochondrial preparation. Representative western blot for cytoplasmic fraction as well as isolated mitochondria from BV2 microglial cells. The figure represents immunoblotting of the cytoplasmic fraction and the isolated mitochondria with COX IV antibody (mitochondrial marker) and GAPDH antibody (cytoplasmic control). The absence of GAPDH bands in the isolated mitochondria indicates minimal cross-contamination and the purity of mitochondrial preparation for subsequent N-glycan analysis. Please click here to view a larger version of this figure.
Figure 4: Mitochondrial N-glycan identification composition determination using IR-MALDESI HRAM mass spectrometry. Glycan mass spectra in the range of 1,700-2,000 m/z showing a significant number of multiply-charged peaks with the annotated structures determined using Glycomod. Abbreviation: IR-MALDESI HRAM = Infrared-Matrix-Assisted Laser Desorption Electrospray Ionization High-Resolution Accurate Mass Analyzer. Please click here to view a larger version of this figure.
Figure 5: Verification of the detected mitochondrial N-glycans. Representative isotopic distributions for four (A-D) mitochondrial N-linked glycans showing an overlay of the observed distribution with theoretical distributions of chlorine and deprotonated adducts. Chi-squared values on the overlaid spectra represent the goodness-of-fit and confirm the detection of N-linked glycans with one and two chlorine adducts. This is further confirmation of the detection of these glycan compositions using IR-MALDESI. Abbreviation: IR-MALDESI = Infrared-Matrix-Assisted Laser Desorption Electrospray Ionization. Please click here to view a larger version of this figure.
Table 1: Solution and buffer recipes used in the protocol. Please click here to download this Table.
Table 2: Multiply charged deprotonated N-linked Glycans detected in the mitochondria with high mass measurement accuracy in Glycomod. Glycan short-hand notation: H = hexose; N = N-acetylglucosamine; F = fucose; S = N-acetylneuraminic acid; Phos = phosphate; Sulph = sulfate modification. Please click here to download this Table.
Microglia are the resident immune cells of the brain, and glycan modifications modulate the immunophenotype and function of microglia. These immune functions demand substantial cellular energy, which is predominantly supplied by mitochondria. Notably, the mitochondrial proteins also present glycan modifications, which have remained significantly understudied due to the technological challenges in investigating sub-cellular glycosylation. Most studies investigating mitochondrial glycosylation rely on lectin-based identification of glycan patterns22, though these approaches are limited by the poor binding specificity of lectins. The essential advances of the technical approach presented in this study are i) reproducible isolation of mitochondrial N-glycans from microglial cells and ii) detection and identification of mitochondrial N-glycans using IR-MALDESI HRAM mass spectrometry. The workflow described here is the first report of the detection of N-glycans released from mitochondrial glycoproteins expressed at physiological levels in microglial cells.
In the present protocol, mitochondrial isolation is maximized by using the reagent-based isolation method. This can be combined with the Dounce homogenization method to improve the mitochondrial yield. A drawback of using the homogenizer compared to the reagent-based isolation is the variation in the force and speed of the pestle between operators, which results in increased experimental variation and reduced reproducibility. Prior studies23,24 have indicated the use of this method and the absence of nuclear (lamin, histone H3) and ER markers (calnexin, Erp57) in the mitochondrial fraction, indicating the purity of the mitochondrial fraction. A potential limitation of the protocol is the requirement of 20 million cells as a starting material for mitochondria isolation. However, the high mitochondrial protein concentration observed in our study allows for a ten-fold scale down of initial microglial cell number for mitochondrial isolation based on the optimization performed in prior studies25,26 (25-250 µg proteins) without losing any N-glycan signals. Furthermore, pooling biological samples to obtain higher cell numbers for mitochondrial isolation could be performed in case of limited protocol scalability to lower cell numbers from primary sources like tissues for efficient glycan detection. In addition, the glycan release step is critical in this protocol. N-glycosidase F (PNGase F) is used to release complete and intact N-linked glycans by hydrolyzing the amide link between the innermost N-acetylglucosamine (GlcNAc) and the asparagine residue27. For N-glycan analysis, it is critical to optimize the activity of PNGase F to achieve full de-glycosylation of the mitochondrial proteins. Protein denaturation using solvent exposure and excess enzyme helps ensure efficient and complete cleavage and release of the N-glycans from the mitochondrial proteins. A digestion time of 18-20 h is optimal for N-glycan release by completing the PNGase F reaction26.
A potential limitation of this protocol is the lack of enrichment of the mitochondrial extract for glycoproteins in this method. While the low-abundance glycoproteins may not be detected in the analysis, this method minimizes the error and bias introduced from lectin affinity purification or chemical enrichment. While IR-MALDESI gives high-confidence identification of the composition of the identified glycans, precise information about the linkages between the glycan residues requires further investigation using tandem mass spectrometry of lithium-adducted glycans to enhance cross-ring cleavages28 or exoglycosidase digestions. Alternatively, LC-MS/MS can be used in addition to or as an alternative to the IR-MALDESI approach, which may provide deeper glycan coverage with more structural details. However, previous studies have shown the correlation between the average ion abundance from IR-MALDESI for metabolites with the absolute quantities determined by LC-MS/MS29, establishing a foundation for direct quantitation of metabolites using IR-MALDESI. The high-throughput nature of IR-MALDESI with an ability to perform MS2 analysis to provide a high-confidence structural confirmation is instrumental for rapid screening of preclinical and clinical samples for potential glycan biomarkers and disease diagnosis. In addition, it should be noted that although the centrifugation of the post-nuclear supernatant at 3000 × g instead of at 12,000 × g minimizes the peroxisomal and lysosomal contaminants, there may still be traces of these proteins present in the mitochondrial preparation.
In conclusion, this study presents a simple, high-throughput method, with minimal sample preparation for the analysis of the mitochondrial glycome in microglial cells and great potential for application in the identification of novel glycan-based therapeutic targets for neurodegenerative diseases. This protocol presents a comprehensive evaluation and standardization of the analytical methods for mitochondrial isolation from microglia and subsequent analysis of the mitochondrial glycome to enable scale-up for large-scale preclinical and clinical studies. This protocol presents several advantages for N-glycan isolation and detection: i) the mitochondrial isolation time for reagent-based protocol is low (≤40 min); ii) the yield of proteins for glycan release is high; iii) same mitochondrial samples prepared for N-glycan analysis can be used for other molecular biological investigations such as proteomic analysis, lectin analysis and mitochondrial flow analysis; and iv) IR-MALDESI HRAM mass spectrometry allows for rapid and improved detection of N-glycans due to the hybrid and soft ionization strategy28 without the need for chemical derivatization of the charged glycans like sialoglycans and sulfoglycans30.
The authors have no conflicts of interest to declare.
The authors would like to thank Seth Eisenberg, graduate student in Muddiman Lab at NCSU, for his help with video recording of mass spectrometric protocol. This research was supported in part by the School of Engineering Innovation Fellows Program at the University of Alabama at Birmingham, AG068309 to D.J.T. and R01GM087964-12 to D.C.M. The schematics in this manuscript were drawn using BioRender.
Name | Company | Catalog Number | Comments |
Equipment | |||
Amersham 600 imager | Cytvia | 29194217 | Gel and membrane imager |
Countess 3 automated cell counter | Fisher Scientific | X003SZ1LY9 | |
Dry Bath Stdrd 4 blck 100-120V | Thermofisher scientific | 88870003 | |
i-Blot2 Gel Transfer Device | Invitrogen | IB21001 | Western blot transfer system |
Inverted microscope | Cell Treat | 04355223EA | |
Microplate reader | 82050-760 | ||
Mini gel tank | Invitrogen | A25977 | |
Open Air Rocker | Fisher Brand | 88861025 | |
Pipet boy | BioTek | 229310 | |
Vortex mixer | Integra- VWR | ||
Mitochondria isolation reagents | |||
Mitochondrial Isolation kit | Thermofisher scientific | 89874 | |
Phosphotase Inhibitor | Thermofisher scientific | 1861274 | |
Protease Inhibitor | Thermofisher scientific | 1861281 | |
N-glycan isolation and IR-MALDESI reagents | |||
Acetic acid | Fisher Scientific | A11350 | 50% in ESI solvent |
Acetonitrile | Sigma Aldrich | 34851-4L | 1 mM in ESI solvent |
Ammonium bicarbonate | Fisher Scientific | A643500 | 100 mM |
Calibration Solution | Thermofisher Scientific | A39239 | Pierce FlexMix |
Dithiothreitol | Sigma Aldrich | AC426380100 | 1 M |
Iodoacetamide | Sigma Aldrich | A322-10VL | |
LC/MS grade water | Thermofisher Scientific | 047146.M6 | |
PNGase F | Bulldog Bio | NZPP010 | 75000 U/mL, enzyme for N-glycan release |
N-glycan isolation and IR-MALDESI consumables | |||
Amicon centrifugal filters | Fisher Scientific | UFC501024 | 10 kDa MWCO |
Mass spectrometer | Orbitrap Exploris 240 | ||
Mid-IR Laser | JGM Associates, Burlington, MA, USA | ||
Teflon microwell slide | Prosolia, Indianapolis, IN, USA | ||
N-glycan analysis softwares | |||
GlycoMod | Expasy | https://web.expasy.org/glycomod/ | |
GlyConnect | Expasy | https://glyconnect.expasy.org/ | |
Protein isolation and western blot consumables | |||
Basix gel loading tips ( 10 µL) | Basix | 13-611-102 | |
Basix gel loading tips ( 200 µL) | Basix | 13-611-116 | |
Cell scrapper | VWR labs | 14-388-100 | |
i-Blot NC regular stacks | Invitrogen | IB23001 | |
i-Blot2 PVDF Regular Stacks | Invitrogen | IB24001 | |
10 µL micropipette | Fisher Scientific | FBE00010 | |
20 µL micropipette | Invitrogen | FBE00020 | |
200 µL micropipette | Fisher Brand | FBE00200 | |
1000 µL micropipette | Fisher brand | FBE01000 | |
10 µL pipet tips | VWR labs | 76322-528 | |
20 µL pipet tips | VWR labs | 76322-134 | |
200 µL pipet tips | VWR labs | 76322-150 | |
1000 µL pipet tips | VWR labs | 76322-154 | |
Well plate | Fisher brand | 14-388-100 | |
Protein isolation and western blot reagents | |||
Actin antibody ( Host : Rabbit ) | Cell Signaling Technologies | 8457T | |
Anti-Rabbit IgG HRP Linked | Cell Signaling Technologies | 7074S | |
Bolt 4-12% Bis-Tris Plus | Invitrogen | NW04120BOX | |
Bovine Serum Albumin | Fisher bioreagents | BP9700-100 | |
COXIV antibody ( Host : Rabbit) | Cell Signaling Technologies | 4844S | |
GAPDH antibody ( Host : Rabbit) | Cell Signaling Technologies | 2118S | |
MicroBCA protein assay Kit | Thermofisher scientific | 23235 | |
Nupage MOPS SDS Runing Buffer [20x] | Thermofisher scientific | NP0001 | |
PAGE Ruler prestained protein ladder | Thermofisher scientific | 815-968-0747 | Dilution= Use 7 µL to load onto first well |
Phosphate buffered saline | Aniara Diagnostics | A12-9423-5 | Prepare 1x PBS from 10x powder |
Pierce ECL Western Blotting Substrate | Thermofisher scientific | 32106 | Chemiluminescent substrate kit |
RIPA Buffer | Thermofisher scientific | 89901 | |
Sample Buffer | Novex | B0007 | The bolt LDS sample buffer is prepared in 3:1 ratio of sample to sample buffer |
Tween-20 | MP Biomedicals | TWEEN201 | |
Tissue culture consumables | |||
Countess Slides | Avantor | 229411 | |
Eppendorf tubes | Cell Treat | 414004-265612-5884 | |
2 mL aspirating pipet | Vista lab | 5090-0010E | |
5 mL serological pipet | Fisher Scientific | 13-678-11D | |
10 mL serological pipet | Basix | 13-678-11E | |
25 mL serological pipet | Vista lab | FB012937 | |
50 mL serological pipet | Vista lab | 14955233 | |
15 mL Conical tube | Avantor | 229225A | |
50 mL conical tube | Cell treat | 4190-0050 | |
T-75 cm2 Tissue culture flask | Fisher Scientific | FB012937 | |
T-180 cm2 Tissue culture flask | Fisher Scientific | FB012939 | |
Tissue culture reagents | |||
BV2 microglial cell line | Creative Bioarray | CSC-I2227Z | Immortalized Mouse Microglia (BV2) derived from C57/BL6 neonatal microglia |
Cell dissociation enzymes | Thermofisher scientific | 12563029 | TrypLE |
Dulbecco's Modified Eagle Medium (DMEM) Low Glucose Media | Gibco | 10567014 | |
Fetal Bovine Serum | Cytiva | SH30071.03HI | |
Minimum Essential Medium (MEM) Non-essential Amino Acids | Gibco | 11140050 | |
Penicillium Streptomycin | Cytivia | SV30010 | |
Phosphate buffer saline | Corning | 21-040-CV | |
Trypan Blue stain 0.4% | Invitrogen | T10282 |
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