2.1 Mycobacterial strains and cultivation
Mtb H37Rv was supplied by R.L. Friedmann (University of Arizona, Tucson, AZ). BCG, MDR Mtb (KMRC-00116-00150), and Mav (KMRC-00800-00012 and-00013) were acquired from the Korean Mycobacterium Resource Center in the Korean Institute of Tuberculosis (Osong, South Korea). Mycobacteria were cultured in Middlebrook 7H9 (Difco, 271310) medium supplemented with 10% oleic albumin dextrose catalase (BD Biosciences, San Diego, CA, 212240), 0.5% glycerol, and 0.05% Tween-80 on a rotary shaking incubator (140 rpm) at 37℃ to an OD600 of 0.4–0.6. Mtb expressing red fluorescent protein (Mtb-ERFP) was cultivated in Middlebrook 7H9 medium supplemented with 10% oleic albumin dextrose catalase, 0.5% glycerol, 0.05% Tween-80, and 50 µg/mL kanamycin (Sigma-Aldrich, St. Louis, MO, 60615). Bacterial cultures were harvested, and the pellets were washed with phosphate-buffered saline (PBS; LPS solution, Daejeon, Korea, CBP007B) by sequential centrifugation at 2090 × g (3000 rpm) for 30 min. To separate bacteria into single cells, pellets resuspended in PBS with 0.1% Tween-80 were subjected to repeated rounds of sonication. The resulting bacterial suspensions were aliquoted and stored at − 80℃. Colony-forming units (CFUs) were counted on Middlebrook 7H10 agar (Difco, 262710).
2.2 Mice
Female wild-type (WT) C57BL/6 mice (Samtako Bio, Gyeonggi-do, South Korea) were obtained at 6–7 weeks of age and maintained under a 12 h:12 h light:dark cycle and specific-pathogen-free conditions. Information on Atg7-floxed mice and Atg7-lacking mice is available elsewhere (28). The mice were 6–8 weeks old at the time of the experiments and were matched by sex. The animal experiments and handling were conducted following the ethical guidelines of Chungnam National University School of Medicine and were approved by the Institutional Animal Care and Use Committee (202109A-CNU-180; Daejeon, South Korea) and the South Korean Food and Drug Administration.
2.3 Isolation of bone marrow-derived macrophages
Bone marrow-derived macrophages (BMDMs) were collected from the femur and tibia of 6–8-week-old WT C57BL/6 mice and cultured for 4–5 days in Dulbecco’s modified Eagle’s medium (DMEM; Lonza, Walkersville, USA, BE12-60fF) supplemented with 10% fetal bovine serum (Gibco, Grand Island, NY, 16000-044) and antibiotics (Lonza, 17-745E) containing 25 ng/mL macrophage colony-stimulating factor (R&D Systems, Minneapolis, MN) at 37℃ in 5% CO2.
2.4 Experimental infection
Bacterial cells stored at − 80℃ were thawed and diluted in Dulbecco’s PBS (DPBS; Cytiva Hyclone™, Marlborough, MA, SH30028.02) containing 0.05% Tween-80. Vial containing bacterial cells was sonicated to a bath sonicator 3 times for 30 sec. Infection of BMDMs and peritoneal macrophages (PMs) at the indicated multiplicities of infection (MOI) of Mtb, BCG, or Mav was conducted for 4 h. The remaining bacteria around cells were removed by washing with DPBS, and infected cells were incubated in fresh DMEM for the indicated times. For in vivo infection, mice were anesthetized and intranasally infected with mycobacteria (Mtb: 5 × 104 CFU/mouse; BCG: 1 × 107 CFU/mouse; Mav: 1 × 106 CFU/mouse; MDR TB: 5 × 103 CFU/mouse). To estimate the bacterial burden, mice were euthanized after 10 days of Mtb, 7 days of BCG, and 10 or 28 days of MDR Mtb infection, and lungs were harvested, homogenized in DPBS, serially diluted, and spotted on 7H10 agar. After incubation for 2–3 weeks, colonies were counted.
2.5 Reagents and antibodies
DMI (592498) and β-cyclodextrin (H5784) were purchased from Sigma-Aldrich. For Western blotting, anti-pSTAT3 (9145S), anti-STAT3 (9139S), and anti-ACTB (5125S) antibodies were purchased from Cell Signaling Technology (Danvers, MA). For immunofluorescence analysis, an anti-LC3A/B (PM036) antibody was obtained from Medical & Biological Laboratories International, and an anti-LAMP1 (SC-19992) antibody was obtained from Santa Cruz Biotechnology. Alexa Fluor 488-conjugated anti-rabbit IgG (A17041) and Alexa Fluor 594-conjugated anti-rabbit IgG (A21207) antibodies were from Molecular Probes. 4’-6-Diamidino-2-phenylindole dihydrochloride (DAPI; D9542) was obtained from Sigma-Aldrich.
2.6 CFU assay
To analyze bacterial survival in murine macrophages, Mtb-, BCG-, or Mav-infected cells (MOI 1) were incubated for 2 h and washed with DPBS to discard extracellular bacteria. The infected cells were incubated in fresh medium for the indicated periods. Thereafter, the cells were lysed in sterile distilled water for 30 min, and intracellular bacteria were collected. Cell lysates were diluted with DPBS and spotted on Middlebrook 7H10 agar containing 10% oleic albumin dextrose catalase. Colonies were counted to assay intracellular bacterial viability after 3 weeks (Mtb and BCG) or 7 days (Mav).
2.7 Histology and immunohistochemistry
Lungs were removed from Mtb-infected mice, fixed in 10% formalin, and embedded in paraffin wax. Paraffin blocks were sectioned (4 µm) and stained with hematoxylin and eosin as described previously (29). The inflamed area was quantified by total field scanning of lung tissues, and the mean fluorescence intensity of the red threshold was examined using FIJI software (ImageJ-win64).
2.8 Determination of dose–response curves
The half-maximal inhibitory concentration (IC50) values were determined following the CLSI guidelines (30). Mtb, BCG, and Mav were cultured in 7H9 medium supplemented with 10% OADC and 0.02% Tween-80 to an OD600 of 0.4–0.6 followed by harvesting, washing twice with PBST, and vortexing 3 times for 5 sec with 30–50 glass beads of diameter 2 mm. Finally, low-speed centrifugation (250 × g) leaves only single bacterial cells in supernatant. Inoculum was prepared from this supernatant. All wells except the negative control (medium only) contained 7H9-OADC with 0.02% Tween-80 and starting inoculum an OD600 of 0.005/mL. DMI, β-cyclodextrin, and INH were two-fold serially diluted 20 times (DMI, β-cyclodextrin) or 10 times (INH) in flat-bottom clear 96-well plates, ranging from 50 mM to 95 nM (DMI) or from 10 µM to 19.5 nM (INH) containing Mtb, BCG, or Mav in a final volume of 100 µL, and then incubated for 5 to 7 days at 37°C. OD600 values were determined using the VersaMax microplate reader (Molecular devices, Sunnyvale, CA). IC50 values were calculated from the OD600 values using Prism 8.0 software (GraphPad Inc., La Jolla, CA).
2.9 RNA preparation and quantitative real-time PCR (qRT-PCR)
Total RNA was isolated from BMDMs, PMs, or lung tissue homogenates using TRIzol reagent (Invitrogen, Waltham, MA, 15596026) in accordance with the manufacturer’s instructions. cDNA was prepared from total RNA using Reverse Transcription Master Premix (ELPIS Biotech, Daejeon, South Korea, EBT-1515) following the manufacturer’s protocols. qRT-PCR was conducted on the Rotor-Gene A 2plex System (Qiagen, Hilden, Germany, 9001620) using cDNA, primer pairs specific to the genes of interest, and SYBR Green Master Mix (Qiagen, 218073) according to the manufacturer’s instructions. Relative mRNA levels were analyzed by the 2−ΔΔ threshold cycle method and normalized to those of Gapdh. The primer sequences used are as follows: Il1b forward: 5′-TGACGGACCCCAAAAGATGA-3′, reverse: 5′-AAAGACACAGGTAGCTGCCA-3′; Il6 forward: 5′-ACAAAGCCAGAGTCCTTCAGA-3′, reverse: 5′-TGGTCCTTAGCCACTCCTTC-3′; Il10 forward: 5′-GCTCTTGCACTACCAAAGCC-3′, reverse: 5′-CTGCTGATCCTCATGCCAGT-3′; Tnf forward: 5′-CCCACGTCGTAGCAAACCAC-3′, reverse: 5′-GCAGCCTTGTCCCTTGAAGA-3′; Gapdh forward: 5′-TGGCAAAGTGGAGATTGTTGCC-3′, reverse: 5′-AAGATGGTGATGGGCTTCCCG-3′.
2.10 Enzyme-linked immunosorbent assay
The supernatant of mouse BMDMs or lung lysates was stored at − 80℃. The levels of the proinflammatory cytokines IL-6 (555240) and IL-10 (555252) were estimated using the Mouse BD OptEIA Set ELISA Kit (BD Biosciences) according to the manufacturer’s instructions.
2.11 Immunofluorescence analysis
BMDMs were grown on coverslips in 24-well plates followed by infection with Mtb-ERFP for 4 h. After treatment, the upper medium was discarded, and cells on coverslips were washed three times in DPBS followed by fixation in 4% paraformaldehyde for 10 min. Thereafter, the cells were permeabilized in 0.25% Triton X-100 for 10 min and incubated overnight at 4℃ with anti-LC3 A/B (1:400 diluted) and anti-LAMP1 (1:400 diluted) primary antibodies. The cells were washed three times with DPBS and reacted for 2 h with the secondary antibody at room temperature. Fluoromount-G in DAPI mounting medium (Thermo Fisher Scientific, Waltham, MA, 00-4959-52) was used to stain nuclei for 5 min.
2.12 Transmission electron microscopy (TEM)
Cells were scraped from plates and collected by centrifugation. Samples were sequentially fixed in 3% glutaraldehyde and 1% osmium tetroxide, cooled on ice for 1 h, washed with 0.1 M cacodylate buffer (pH 7.2) containing 0.1% CaCl2, and dehydrated in an ethanol and propylene oxide series. Next, samples were embedded in Epon 812 mixture and polymerized at 60°C for 36 h. Using the ULTRACUT UC7 ultramicrotome (Leica Biosystems, Vienna, Austria), sections of 70 nm thickness were cut and mounted on 75-mesh copper grids. Sections were counterstained with uranyl acetate and lead citrate for 10 min and 7 min, respectively, and examined using the KBSI Bio-High Voltage EM (JEM-1400 Plus at 120 kV and JEM-1000BEF at 1000 kV; JEOL Ltd., Tokyo, Japan).
2.13 Western blotting
BMDM lysates were collected in Protein 5× Sample Buffer (ELPIS BIOTECH, EBA-1052) diluted with RIPA buffer (150 mM sodium chloride, 1% Triton X-100, 0.1% SDS, 1% sodium deoxycholate, 50 mM Tris-HCl at pH 7.5, and 2 mM EDTA) supplemented with protease (04693132001) and phosphatase (11836170001) inhibitor cocktails (Roche, Mannheim, Germany). Samples were boiled for 10 min on a heating block and cooled on ice for 10 min. The samples were resolved by SDS-PAGE and transferred to a nitrocellulose (Pall Corporation, NY, 66485) or PVDF (Millipore, Burlington, MA, IPVH0001) membrane at 200 mA for 2 h. To prevent nonspecific binding, membranes were incubated in blocking solution with 1% BSA in TBS containing 0.1% Tween 20 for 30 min at room temperature and reacted overnight with anti-pSTAT3, -STAT3, or -ACTB primary antibody at 4℃. The membranes were reacted with the appropriate horseradish peroxidase-conjugated secondary antibodies (7076S [anti-mouse IgG], 7074S [anti-rabbit IgG], Cell Signaling Technologies) for 1 h at room temperature. Immunoreactive bands were visualized with ECL reagent from the Chemiluminescence Assay Kit (Millipore, WBKL S0500), and the appropriate bands were detected using the UVitec Alliance mini-chemiluminescence device (UVitec, Rugby, UK). Band intensities were measured using Image J software and normalized to that of β-actin.
2.14 Statistical analysis
Statistical analysis was conducted using Prism 8.0 for Windows (GraphPad Software Inc., San Diego, CA). The unpaired Student’s t-test was used to compare two groups and two-way ANOVA for three or more groups. Data are means ± standard deviation or ± standard error of the mean. Statistical significance is indicated as * P < 0.05, ** P < 0.01, and *** P < 0.001.