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11 protocols using cxnft

1

Immunofluorescence Analysis of Autophagy Markers

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After H290 and 8A cells were treated with PAL, they were then incubated for 8 h/37 °C. The cells were then fixed with 4% (w/v) paraformaldehyde for 10 min/RT, washed 3 times using PBS, incubated with 0.1% (v/v) Triton X100 and blocked for 1 h at RT with 3% (w/v) bovine serum albumin. The cells were then incubated overnight at 4 °C with primary antibodies against iNOS (Cat. #CXNFT; 1/200 dilution; Invitrogen), p65 (Cat. #D14E12; 1/400 dilution; Cell Signaling Technology), LAMP1 (Cat. #ab25630; 1/500 dilution; Abcam), LC3B (Cat. #D11; 1/1000 dilution; Cell Signaling Technology), SQSTM1/p62 (Cat. #D5L7G, 1/1000 dilution; Cell Signaling Technology), TFEB (Cat. #1337-I-AP, 1/100 dilution; Proteintech) and NF-κB (Cat. #PA5-88084, 1/500 dilution; Thermofisher), washed 3 times with PBS and incubated with the secondary antibodies, Alexa Fluor® Plus 488 or Alexa Fluor® Plus 568 (Invitrogen). A Zeiss confocal microscope (LSM880, Carl Zeiss) was used to observe cellular morphology. The fluorescence intensity and Mander's overlap for image co-localization were measured using ImageJ 4.7v software. Fifty cells were quantified with ImageJ software for integration of each fluorescence (wavelength) area via excluding the cellular background. Relative intensities per cell in arbitrary units are shown.
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2

Immune Checkpoint Therapy in Mice

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For immune checkpoint therapy, rat IgG2a αPD1 (RMP1-14, Leinco)
and murine IgG2b αCTLA4 (9D9, Leinco Technologies) were used. Mice were
injected intraperitoneally with 200μg of each antibody on 3, 6 and 9 days
post tumor transplant. Antibodies used for multi-color flow cytometry were CD45
(30-F11), CD11b (M1/70), Thy1.2 (30H12), CD4 (RM4-5), CD8β (YTS156.7.7),
I-E/I-A (M5/114.15.2), CD64 (X54-5/7.1), Ly6G (1A8), T-BET (4B10), CD150/SLAM
(TC15-12F12.2), KLRG1 (2F1), ICOS (15F9), CD44 (IM7), PD-1 (29F.1A12),
SIINFEKL-H-2-Kb (25-D1.16) (BioLegend), CD24 (M1/69), F4/80
(T45-2342) (BD Biosciences), FOXP3 (FJK-16s, eBiosciences) and iNOS (CXNFT,
Invitrogen). Zombie NIR (BioLegend) was used to stain for cellular viability.
The BD Cytofix/Cytoperm Plus kit (BD Biosciences) was used following
manufacturer’s protocol for intracellular staining of iNOS, T-BET and
FOXP3.
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3

Immune Checkpoint Therapy in Mice

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For immune checkpoint therapy, rat IgG2a αPD1 (RMP1-14, Leinco)
and murine IgG2b αCTLA4 (9D9, Leinco Technologies) were used. Mice were
injected intraperitoneally with 200μg of each antibody on 3, 6 and 9 days
post tumor transplant. Antibodies used for multi-color flow cytometry were CD45
(30-F11), CD11b (M1/70), Thy1.2 (30H12), CD4 (RM4-5), CD8β (YTS156.7.7),
I-E/I-A (M5/114.15.2), CD64 (X54-5/7.1), Ly6G (1A8), T-BET (4B10), CD150/SLAM
(TC15-12F12.2), KLRG1 (2F1), ICOS (15F9), CD44 (IM7), PD-1 (29F.1A12),
SIINFEKL-H-2-Kb (25-D1.16) (BioLegend), CD24 (M1/69), F4/80
(T45-2342) (BD Biosciences), FOXP3 (FJK-16s, eBiosciences) and iNOS (CXNFT,
Invitrogen). Zombie NIR (BioLegend) was used to stain for cellular viability.
The BD Cytofix/Cytoperm Plus kit (BD Biosciences) was used following
manufacturer’s protocol for intracellular staining of iNOS, T-BET and
FOXP3.
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4

Tumor Immune Cell Phenotyping by Flow Cytometry

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For ow cytometry analysis, the harvested tumors from each group were minced and incubated for 1 h at 37°C in a digestion buffer comprising 2 mg/ml collagenase D (Roche) and 40 μg/ml DNase I (Roche). Cell suspensions were ltered through a 70 μm cell strainer (Corning) and incubated for 3 min at room temperature in ACK lysis buffer (Gibco) to remove the cell clumps and red blood cells. After washing with FACS buffer (1% FBS in PBS), the cells were ltered through a nylon mesh. Next, the cells were incubated on ice for 30 min in Fixable Viability Dye eFluor TM 450 (Invitrogen) to exclude the dead cells before antibody staining. Then, the cells were washed with FACS buffer and incubated on ice for 30 min in FACS buffer with surface antibodies targeting CD45 (30-F11, Invitrogen), CD3 (17A2 or 145-2C11, Invitrogen), CD8a (53-6.7, Invitrogen), CD4 (RM4-5, Invitrogen), PD-1 (J43, Invitrogen), CD25 (PC61.5, Invitrogen), ICOS (7E.17G9, Invitrogen), CD11b (M1/70, Invitrogen), Ly-6G (RB6-8C5, Invitrogen), F4/80 (BM8, Invitrogen), or Ly-6C (HK1.4, Invitrogen). Cells were further permeabilized using a Foxp3 Staining Buffer kit (Invitrogen) and stained for Foxp3 (FJK-16s, Invitrogen), iNOS (CXNFT, Invitrogen), or Arginase 1 (A1exF5, Invitrogen). The stained cells were analyzed using a CytoFLEX ow cytometer (Beckman Coulter), and the data were analyzed with the FlowJo software (Tree Star Inc.).
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5

Single-Cell Isolation from Organoids

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organoids were washed with warm PBS and then incubated with TrypLE Express (Gibco) for 10–15 minutes. Organoids were scraped from the plate and separated into single cells by repeated pipetting. Organoid-derived IECs were washed in PBS, treated with anti-CD16/32 and then stained with antibodies as described above for primary IECs. For intracellular staining of iNOS, organoids were fixed and permeabilized using BD Fix/Perm kit before staining with anti-iNOS antibody (Invitrogen clone CXNFT).
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6

Immunofluorescent Imaging of Spleen Tissue

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Spleen biopsies were submerged in PLP buffer (1% paraformaldehyde, 75mM sodium phosphate monobasic, 75mM disodium phosphate, 50mM L-Lysine and 10mM sodium periodate) overnight at 4°C, washed three times in PBS and then dehydrated in 30% (w/v) sucrose overnight. Fixed tissues were then stored at -80°C in OCT Compound (Tissue-Tek) until use. A Leica cryostat was used to cut fixed and frozen tissues at 10μm thickness and mounted onto SuperFrost Plus slides. Sections were permeabilised with 0.3% Triton X-100, 0.1M glycine, 0.1% cold fish skin gelatin and 1% BSA in PBS for 10 min, blocked with serum-free protein block (Agilent) for 1hr, and then stained with fluorescently-conjugated mAbs against iNOS Alexa Fluor 488 (CXNFT, ThermoFisher), CXCL9 eFluor 660 (MIG-2F5.5, ThermoFisher), CD4 CF-594 (RM4-5, BD Bioscience) and B220 Pacific Blue (RA3-6B2, BioLegend) for 1hr, all at room temperature. Stained tissue sections were mounted with ProLong Gold Antifade Mountant (ThermoFisher) and imaged using a Zeiss LSM780 confocal microscope. Images were analysed using the Fiji software [81 (link)].
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7

Phenotypic Characterization of Innate Immune Cells

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Cells were blocked for Fc receptors with anti-mouse CD16/32 antibodies. For surface staining, cells were stained on ice for 30 mins with the following fluorescent conjugated antibodies: fluorescein isothiocyanate (FITC)–anti-Ly6G (1A8, Biolegend), peridinin-Chlorophyll-Protein Complex (PerCP)-anti-Ly6C Abs (HK1.4, Biolegend), phycoerythrin (PE)-anti-CD11b (M1/70, Biolegend) or allophycocyanin (APC)–anti-CD11b (M1/70, Biolegend). Staining for intracellular iNOS with APC–anti-iNOS (CXNFT, ThermoFisher scientific) was performed after fixation and permeabilization of the cells with a Cytofix/cytoperm kit (BD). Neutrophils were identified as CD11b+Ly6G+, and monocytes were identified as CD11b+Ly6G-Ly6C+ (Supplementary Figures 14). For in vitro phagocytosis assays, peritoneal cells were incubated with PE-labeled Escherichia coli (Abcam) for 2 hours, then these cells were recollected and labeled with surface markers CD11b, Ly6G, and Ly6C to identify monocytes. For ROS detection, peritoneal cells were incubated in a complete medium containing 5μM/ml ROS Brite™ (AAT Bioquest) for 30 minutes 37℃and then was stained with surface markers CD11b, Ly6G, and Ly6C to identify monocytes. Flow cytometry analysis was performed using the BD Accuir C6 Plus cell analyzer (BD Biosciences).
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8

Multiparameter Flow Cytometry Analysis of Macrophages

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All antibodies were purchased from Biolegend UK unless otherwise indicated. Equal numbers of cells were stained with LIVE/DEAD cell viability assay (Life Technologies) and blocked with 5 μg/mL anti CD16/32 (2.4G2, BD Biosciences) and heatinactivated normal mouse serum (1:10) in FACS buffer (0.5% BSA and 2 mM EDTA in Dulbecco’s PBS) before surface staining with antibodies to F4/80 (BM8), SiglecF (E502440), Ly6C (HK1.4), Ly-6G (1A8), TCRβ (H57-597), CD11b (M1/70), CD11c (N418), I-A/I-E (M5/114.15.2), CD19 (6D5) and CD115 (AFS98). Detection of intracellular Ym1 and NOS2 was performed directly ex vivo. Cells were stained for surface markers then fixed with 2% paraformaldehyde (Sigma Aldrich), permeabilized using Permeabilization Buffer (eBioscience) and stained with directly labeled antibodies to NOS2 (CXNFT; eBioscience) or biotinylated polyclonal goat antiYm1 (R&D Systems) followed by streptavidin-PerCP (Biolegend). Expression of Ym1 and NOS2 was determined relative to appropriate polyclonal or monoclonal isotype controls.
Samples were acquired on a BD LSR II using BD FACSDiva software (BD Bioscience) and post-acquisition analysis performed using FlowJo v9 software (Tree Star Inc.). Macrophages were identified as lineage negative (CD19-,TCRb-,Ly6G-,SiglecF-), CD11b+ CD115+.
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9

Characterizing Myeloid Cells in Infected Lungs

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Myeloid cell populations from infected lungs were characterized using flow cytometry. For cell surface staining, Abs against CD11b (M1/70; eBioscience), CD11c (N418), Ly6G (1A8), and Ly6C (HK1.4; all from BioLegend) were used. For intracellular staining of NOS2, lung cells were fixed with 2% paraformaldehyde and permeabilized with 0.5% saponin (Sigma) before staining with anti-NOS2 Ab (CXNFT; eBioscience). Samples were acquired on a LSR II flow cytometer with FACSDiva software (BD Bioscience). Data were analyzed using FlowJo software (TreeStar).
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10

Multiparametric Flow Cytometry Analysis

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Single cell suspensions from tumors and spleens were incubated for 5 min with Fc-block (BD Biosciences) and then stained with either a myeloid panel of antibodies comprising CD45-BV786 (Clone 30-F11, BD Biosciences), GR1-PE (Clone RB6-8C5, BD Biosciences), CD11b-BV711 (Clone MI/70, BD Biosciences), Ly6C-PerCpCy5.5 (Clone AL-21, BD Biosciences), Ly6G-FITC (Clone IA8, BD Biosciences) and DAPI (Invitrogen) or a lymphoid panel of antibodies comprising CD45-AlexaFlur700 (Clone 30-F11, BD Biosciences), CD3-PE (Clone 145-2C11, eBioscience), NKp46-PE-Cy7 (Clone 29A1.4, eBioscience), CD4-APC (Miltenyi Biotec), CD8-FITC (Miltenyi Biotec), CD44-BV711 (Clone IM7, BD Biosciences), CD62L-BV786 (Clone MEL-14, BD Biosciences), PD-1-BV605 (Clone J43, BD Biosciences) and DAPI (Invitrogen). In some experiments MDCSs were also analyzed for iNOS-PE (Clone CXNFT, eBioscience) expression. Cells were acquired on a BD LSRFortessa and analyzed using FACSDiva.
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