Ethics statement.
This study was conducted in accordance with the Helsinki Declaration and has been approved by the Ethics Committee of Beijing Chest Hospital, Capital Medical University (Ethics No: scientific research 2023 (44)). All subjects signed written informed consent forms.
Subjects and sample collection
Patients diagnosed with PTB at Beijing Chest Hospital, Capital Medical University, from June 2023 to February 2024 were divided into severe and non-severe groups. The inclusion of the severe PTB group requires meeting any one of the following four criteria: (1) Resting oxygen saturation ≤ 93% when breathing air; (2) Oxygenation index (arterial oxygen partial pressure/oxygen concentration) ≤ 300 mmHg, or arterial oxygen partial pressure ≤ 60 mmHg when breathing air at rest; (3) Chest imaging shows TB lesions in both lungs accumulating over more than half of the lungs; (4) If a patient meets one of the above inclusion criteria and experiences shock or organ failure, ICU monitoring and treatment are required. Patients who do not meet the criteria for severe patients at the same time are classified as non-severe patients. According to the criteria, 30 cases each of severe tuberculosis (STB), non-severe tuberculosis (NSTB) patients, and healthy controls (HC) were included, with HC from Changping Physical Examination Center in Beijing. Subjects were matched for age and gender. Subjects had fasting blood samples collected in EDTA anticoagulant tubes on the first day of hospitalization, centrifuged at 4,500 rpm for 10min, and the plasma stored at -80°C.
UHPLC-MS/MS analysis
100 µl plasma was thoroughly mixed with 400 µl of cold methanol acetonitrile (v/v, 1:1) via vortexing. And then the mixture were processed with sonication for 1 h in ice baths. The mixture was then incubated at -20°C for 1 h, and centrifuged at 4°C for 20 min with a speed of 14,000g. The supernatants were then harvested and dried under vacuum LC-MS analysis. Metabolomics profiling was analyzed using a UPLC-ESI-Q-Orbitrap-MS system (UHPLC, Shimadzu Nexera X2 LC-30AD, Shimadzu, Japan) coupled with Q-Exactive Plus (Thermo Scientific, San Jose, USA). For liquid chromatography (LC) separation, samples were analyzed using a ACQUITY UPLC® HSS T3 column (2.1×100 mm, 1.8 µm) (Waters, Milford, MA, USA). The flow rate was 0.3 ml/min and the mobile phase contained: 0.1% FA in water (A) and 100% acetonitrile (B). The gradient was 0% buffer B for 2 min and was linearly increase to 48% in 4 min, and then up to 100% in 4 min and maintained for 2 min, and then decreased to 0% buffer B in 0.1 min, with 3 min re-equilibration period employed. The electrospray ionization (ESI) with positive-mode and negative mode were applied for MS data acquisition separately. The raw MS data were processed using MS-DIAL for peak alignment, retention time correction and peak area extraction. The metabolites were identified by accuracy mass (mass tolerance < 10 ppm) and MS/MS data (mass tolerance < 0.02 Da) which were matched with HMDB, massbank and other public databases and our self-built metabolite standard library. In the extracted-ion features, only the variables having more than 50% of the nonzero measurement values in at least one group were kept.
Isolation of peripheral blood mononuclear cells
Blood samples were collected from 30 patients with STB and 30 patients with NSTB, and peripheral blood mononuclear cells (PBMCs) were isolated for subsequent RNA extraction and RT-qPCR. PBMCs were isolated and stored at -80℃ using the instructions provided in the Peripheral Blood Lymphocyte Separation Fluid (TBD, Tianjin, China, #LTS1977) manual. Separate PBMCs from 10ml whole blood and 1 ml of serum-free cell freezing solution (CELLSAVING, Suzhou, China, #C854497) was added to the isolated PBMCs before storage. Concurrently, record the patient's uric acid results.
Cell counting kit-8 assay (CCK-8)
THP-1 cells were seeded in a 96-well plate at a density of 5 × 104 cells/well and induced by 0.1 µg/ml PMA(Sigma, USA, #P8139) for 12 h to differentiate into macrophages. Different concentrations (0, 0.05, 0.1, 0.2, 0.4, 1, 2 mM) of allopurinol (AP, Sigma, USA, #A8003) solution were added to the cells. The AP stock solution was prepared by adding 10 mg of AP powder to 7.347 ml of DMSO (Sangon Biotech, Shanghai, China, #A503039-0250). After 24 h of cell stimulation, 10 µL of CCK-8 solution (Beyotime, Shanghai, China, #C0048S) was added to each well and incubated in the dark for 4 h. The OD value at 450 nm was measured using an enzyme-linked immunosorbent assay (ELISA) reader (Bio Tek, USA).
Macrophages infection and colony-forming unit counting
THP- 1 originated from the American Type Culture Collection (ATCC) and was grown in Roswell Park Memorial Institute (RPMI) medium (Gibco, Carlsbad, CA, USA, #8117072) with 10% fetal calf serum (Gibco, #2045512CP) at 37°C in 5% CO2.The cells were seeded in a 12-well plate at a cell density of 5×105 cells/ml. THP-1 cells were induced with 0.1 µg/ml PMA. The cells were then washed and incubated in fresh culture medium without PMA for an additional 24 h.The MTB H37Rv strain, sourced from ATCC in Manassas, VA, USA, was cultivated in Middlebrook 7H9 broth (BD, USA, #371301) supplemented with 10% OADC (oleic acid-albumin-dextrose-catalase) and 0.05% Tween-80 (Sigma, USA, #P1754) for a period of 2 to 3 weeks. Subsequently, the culture was transferred to a neutral Roche solid medium (BASO, Guangdong, China, #BA7005D-2) for an additional 3 to 4 weeks. Bacterial colonies were harvested from the solid medium using a sterile loop and placed into a grinding bottle. To ensure a uniform dispersion, a homogeneous bacterial suspension was prepared using an ultrasonic disperser. This suspension was then diluted with 1×PBS (Solarbio, Beijing, China, #P1003) to achieve an optical density (OD) at 600 nm of 0.3, which corresponds to a concentration of 1 x 107 colony-forming units (CFUs) per milliliter of MTB. Macrophage cells were infected with 2.5 x 106 CFUs of MTB to achieve a multiplicity of infection (MOI) of 10 for 2 h at 37°C. Afterward, remove the culture medium for ELISA, and the cells were washed three times with 1×PBS to eliminate non-internalized bacteria, followed by incubation with fresh medium. The experiment was conducted in two groups: a control group and an experimental group. The control group was treated with DMSO, while the experimental group was treated with AP. Samples were collected at 0, 4, 8, and 24 h, with the 0 h point representing the uninfected state. To enumerate the intracellular bacteria, cells were lysed by adding 500 µl of 0.05% sodium dodecyl sulfate (SDS) to each well for 10 min. The lysed mixture was then serially diluted with 1×PBS, and the diluted samples were spread on Middlebrook 7H10 agar (BD, USA, #220959) supplemented with 10% OADC. The plates were incubated at 37°C for 3 to 4 weeks, after which the colonies were counted.
ROS detection
ROS detection was performed according to the instructions of the Reactive Oxygen Species Assay Kit (Yeasen, Shanghai, China, #50101ES01). The culture medium containing the bacterial suspension was removed from the wells, and the wells were washed with serum-free RPMI 1640 medium. The appropriate working solution of DCFH-DA (1:1000) was added to the wells, and the plate was incubated at 37℃ in the dark for 30 min. The wells were then washed 1–2 times with serum-free culture medium, and the fluorescence intensity was measured at an excitation wavelength of 488 nm and an emission wavelength of 525 nm using a multi-function microplate reader (Bio Tek, USA).
RT-qPCR
Extract total RNA from macrophage samples collected at various infectious time points and PBMCs of subjects. Reverse transcription was performed using the Hifar II 1st Strand cDNA Synthesis Kit (Yesen, Shanghai, China, #11119ES) according to the manufacturer's instructions. Gene expression was measured using the QuantiNova SYBR PCR Mix Kit (QIAGEN, Shanghai, China, #208252) on a 7500 real-time fluorescence quantitative PCR system. GADPH was used as the internal reference, and the relative expression levels of the genes were normalized to GADPH using the 2−ΔΔCt method. The gene names and primers required for the experiment are listed in Table S1.
ELISA
Cell supernatants collected at different time points before and after infection and plasma were used to measure the concentrations of TNF-α (NEOBIOSCIENCE, Guangdong, China, #EHC103a.96), IL-1β (BBI, Shanghai, China, #D711068-0096), and IL-6 (BBI, Shanghai, China, #D7113918-0096) using ELISA kits according to the manufacturer's protocol.
Western blot
RIPA lysis buffer (Beyotime, Shanghai, China) containing protease and phosphatase inhibitors (Solarbio, Shanghai, China, #P1260) was added to the wells. The BCA protein assay kit (Beyotime, Shanghai, China, #P0012) was used to quantify the protein concentration. The protein samples were loaded onto a 12% SDS-PAGE gel, transferred to a PVDF membrane (Millipore, Shanghai, China, IPVH00010), and blocked with 5% BSA at room temperature for 1.5 h. The membrane was then incubated overnight at 4°C with antibodies against NF-κB p65 (Cell Signalling Technology, Shanghai, China, #9609), phospho-NF-κB p65 (Cell Signalling Technology, Shanghai, China, #3033), and β-actin (Cell Signalling Technology, Shanghai, China, #3700). After washing with TBST, the membrane was incubated with HRP-conjugated anti-rabbit IgG (Cell Signalling Technology, Shanghai, China, #7074) or anti-mouse IgG (Cell Signalling Technology, Shanghai, China, #7076) secondary antibodies at room temperature for 1 h. The specific membranes were visualized using a chemiluminescence imaging system (GelView 6000Plus, Guangzhou, China).
Data Processing and Statistical Analysis
R (version:4.0.3) and R packages were used for all multivariate data analyses and modeling. Data were mean-centered using Pareto scaling. Models were built on principal component analysis (PCA), orthogonal partial least-square discriminant analysis (PLS-DA) and partial least-square discriminant analysis (OPLS-DA). OPLS-DA allowed the determination of discriminating metabolites using the variable importance on projection (VIP). Parameter R2Y (the model's interpretability towards the categorical variable Y) and Q2 (the model's predictability) are used to evaluate the effectiveness of the model. Finally, by randomly changing the order of the categorical variable Y multiple times, different random Q2 values are obtained to further test the effectiveness of the model. Metabolites with VIP values greater than 1.0 and P values less than 0.05 were considered statistically significant. To identify the perturbed biological pathways, the differential metabolite data were performed KEGG pathway analysis using KEGG database (http://www.kegg.jp). KEGG enrichment analyses were carried out with the Fisher’s exact test, and FDR correction for multiple testing was performed. Enriched KEGG pathways were nominally statistically significant at the P < 0.05 level.Statistical analysis of the experimental results was performed using GraphPad Prism 8 software. Unpaired t-test or one-way ANOVA was used for intergroup comparisons. Chi-square test and Kruskal-Wallis H test were used for non-parametric analysis of three or more groups. A P-value less than 0.05 was considered statistically significant, and the significance levels were denoted by asterisks (*, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001).