2.1. Main reagents and consumables.
The primary reagents used in the LC-MS/MS analysis included Nanosep Centrifugal Devices 10 kD (Pall) and the iTRAQ 8 plex kit (SCIEX). For Western blot analysis, the following antibodies were used: anti-SP1 (ab231778; Abcam, USA), anti-TRIM24 (4208-1-AP; Proteintech, USA), anti-CLTCL1 (22283-1-AP; Proteintech, USA), anti-VAV1 (AF6182; Affinity, USA), anti-WDR70 (PU451766S; Abmart, Shanghai, China), anti-MYO1G (LK43614S; Abmart, Shanghai, China), anti-Actin (Cell Signaling, USA), goat anti-rabbit IgG (SA00001-2; Proteintech, USA), and goat anti-mouse IgG (074-1806; KPL, USA). Norcantharidin was obtained from Shanghai Yuanye Bio-Technology Co., Ltd (5442-12-6).
2.2. Cell culture
THP-1 cells (Laboratory conservation) were maintained in RPMI-1640 (Solarbio) supplemented with 10% FBS (WISENT, Canada), 100 U/mL penicillin, and 100 µg/mL streptomycin at 37°C and 5% CO2. All media components and reagents were endotoxin-free.
2.3. Macrophage phenotype induction and Mycobacterium tuberculosis H37Ra Intracellular infection
THP-1 monocytes were cultured in a 10 cm diameter petri dish with 10^7 cells per well and induced to the macrophage phenotype by exposure to 1 µg/mL Phorbol 12-Myristate 13-Acetate (PMA, MultiSciences) for 24 hours. Twenty-four hours after washing off PMA and incubating in complete medium (DMEM supplemented with 10% FBS), the cells were exposed to 10^8 colony forming units (CFU) of Mtb H37Ra (MOI = 10) in antibiotic-free medium for 6 hours. The cells were then washed three times with PBS to remove extracellular bacteria and incubated in complete medium with Norcantharidin (5 µg/mL or 10 µg/mL) for 24 hours. Afterwards, the cells were rinsed three times with PBS, 1 mL of fresh PBS was added, and the cells were scraped off, centrifuged, and the supernatant was discarded. The cell pellets were stored at -80°C for subsequent use. Protein extraction using RIPA was performed for Western blot analysis.
2.4. Workflow overview of iTRAQ
iTRAQ labeling technology is a widely used method in quantitative proteomics research. It consists of reporter groups, balance groups, and reactive groups. The total molecular weight of the reporter group plus the balance group is 305 Da. Isotopically labeled molecules have identical molecular weights and chemical properties. The reactive group reacts with both N-terminal amino groups of enzymatically cleaved peptides and lysine side chain amino groups, achieving an efficiency exceeding 99%. Enzymatically cleaved peptides from different samples are reacted with iTRAQ reagents labeled with distinct tags before being mixed together. In primary mass spectrometry analysis by LC-MS, peptides from various sources have identical mass-to-charge ratios. In secondary mass spectrometry analysis, reporter groups detach from peptide chains to reflect relative quantitative information about proteins in each sample (Fig. 1).
2.5. Protein Extraction
Protein extraction was performed by homogenizing 10^7 cells in 200 µL of lysis buffer (RIPA containing 1% PMSF) on ice for 30 minutes and then centrifuged (10,000 × g for 5 minutes at 4°C). The supernatants were quantified using the Pierce BCA Protein Assay Kit. All analyses were performed in duplicate. Samples were stored at − 80°C for further analysis.
2.6. Enzymatic digestion and iTRAQ labeling in protein sample solution.
Each iTRAQ reagent (AB Sciex, USA) was dissolved in 70 µL of isopropanol and added to the respective peptide mixture for 120 minutes. The labeling reaction was quenched by the addition of 100 µL of Milli-Q water, and the seven labeled samples were then pooled into one sample according to the manufacturer’s instructions. After pooling, the samples were evaporated by vacuum concentration to remove excess water, TEAB, and isopropanol. Aliquots of lysates were mixed with 200 µL of 8M urea in Nanosep Centrifugal Devices (PALL). The device was centrifuged at 14,000 × g at 20°C for 20 minutes. All following centrifugation steps were performed under the same conditions to ensure maximum concentration. The concentrate was diluted with 200 µL of 8M urea in 0.1M Tris-HCl, pH 8.5, and the device was centrifuged. Proteins were reduced with 10 mM DTT for 2 hours at 56°C. Subsequently, the samples were incubated in 5 mM iodoacetamide for 30 minutes in the dark to block reduced cysteine residues followed by centrifugation. The resulting concentrate was diluted with 200 µL of 8M urea in 0.1M Tris-HCl, pH 8.0, and concentrated again. This step was repeated twice, and the concentrate was subjected to proteolytic digestion overnight at 37°C. The digests were collected by centrifugation.
2.7. LC-MS/MS analysis
The lyophilized peptide fractions were re-suspended in ddH2O containing 0.1% formic acid, and 2 µL aliquots were loaded into a nanoViper C18 trap column (Acclaim PepMap 100, 75 µm × 2 cm). Chromatography separation was performed on the Easy nLC 1200 system (Thermo Fisher). The trapping and desalting procedures were carried out with 20 µL of 100% solvent A (0.1% formic acid). Then, an elution gradient of 5–38% solvent B (80% acetonitrile, 0.1% formic acid) over 60 minutes was used on an analytical column (Acclaim PepMap RSLC, 75 µm × 25 cm C18-2 µm 100 Å). Data-dependent acquisition (DDA) mass spectrometry techniques were used to acquire tandem MS data on a Thermo Fisher Q Exactive mass spectrometer fitted with a Nano Flex ion source. Data was acquired using an ion spray voltage of 1.9 kV and an interface heater temperature of 275℃. For a full mass spectrometry survey scan, the target value was 3 × 10^6, and the scan range was 350 to 2,000 m/z at a resolution of 70,000 with a maximum injection time of 100 ms. For the MS2 scan, only spectra with a charge state of 2–5 were selected for fragmentation by higher-energy collision dissociation with a normalized collision energy of 28. The MS2 spectra were acquired in the ion trap in rapid mode with an AGC target of 8,000 and a maximum injection time of 50 ms. Dynamic exclusion was set for 25 seconds.
2.8. Protein Identification
Peptides were analyzed using high-performance liquid chromatography tandem high-resolution mass spectrometry after labeling with iTRAQ reagent and subsequent enrichment, generating substantial mass spectrum data. PD software was used for protein identification in the samples under the following conditions: PSM FDR (false positive) < 0.01 and Protein FDR < 0.01. Protein identification was performed using the human Uniprot sequence database (20399), with the database sequence file located at data/1.Identification/Uniprot-human.fasta.
2.9. The annotation of differentially functional proteins.
Protein annotation involved using multiple functional databases, such as REACTOME and KEGG, to annotate the functions of identified proteins and reveal their functional classifications.
2.10. Network and Functional Analysis
To analyze the involvement of differentially regulated proteins in common biological processes, an enrichment ontology and pathway analysis was performed using g:Profiler software (version e104_eg51_p15_3922dba) based on REACTOME and KEGG databases (p-adjusted < 0.05).
2.11. Validation of LC-MS/MS Results by Western Blot
To validate the LC-MS/MS results, we performed a Western blot analysis for six chosen proteins (CLTCL1, VAV1, SP1, TRIM24, MYO1G, and WDR70) selected from the list of significantly changed proteins. The protein extract was used for Western blot analysis. Actin was used as a control for equal loading and to quantify the relative abundance of the examined proteins. Forty micrograms of total protein isolates were solubilized in a sample buffer (100 mM Tris-HCl, 4% SDS, 20% glycerol, 0.2% bromophenol blue, and 200 mM dithiothreitol, pH 6.8) and incubated for 7 minutes at 99.9℃. Samples were separated by SDS-PAGE electrophoresis and transferred onto a polyvinylidene fluoride (PVDF) membrane (Millipore, Ireland). A 5% BSA solution in TBST was used to block nonspecific binding. Next, the membranes were incubated at 4℃ overnight with specific primary antibodies: SP1 (1:1000; ab231778; Abcam, USA), TRIM24 (1:1000; 14208-1-AP; Proteintech, USA), CLTCL1 (1:1000; 22283-1-AP; Proteintech, USA), VAV1 (1:1000; AF6182; Affinity, USA), WDR70 (1:500; PU451766S; Abmart, Shanghai, China), MYO1G (1:500; LK43614S; Abmart, Shanghai, China), and actin (1:3000; Cell Signaling, USA). After washing, membranes were incubated with HRP-conjugated secondary antibodies (1.5 hours, RT): goat anti-rabbit IgG (1:5000; SA00001-2, Proteintech, USA) for CLTCL1 (CHC22: clathrin heavy chain 22), VAV1, SP1, TRIM24, MYO1G, and WDR70, and goat anti-mouse IgG for actin (1:5000; 074-1806, KPL, USA). Visualization of immunocomplexes was carried out using chemiluminescence HRP substrate (Merck Millipore, Burlington, MA, USA) according to the manufacturer’s protocol and visualized with an AI 680 Imaging System (GE, USA). The results were quantified by optical density (OD) analysis of immunocomplexes with Image J (National Institutes of Health, USA). Data were presented as a ratio of examined protein relative to actin protein in arbitrary OD units. The normality of Western blot data distributions was confirmed using a Shapiro–Wilk test (p > 0.05), and the results were statistically checked by a Student’s t-test (p < 0.05) using Statistica software (GraphPad Prism 8, USA). Data were presented as mean ± SEM (n = 5).
2.12. Statistical analysis
A normality test was first performed to determine whether our dataset followed a normal distribution. Student’s t-test for two-sample and two-tailed comparisons was used with GraphPad Prism version 8.0 (GraphPad Software Inc., San Diego, CA, USA). In all cases, P < 0.05 was considered statistically significant.