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8 protocols using anti t bet

1

Transcription Factor Binding Assay

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ONP assays were conducted as previously described 51 (link). Briefly, nuclear extracts were
precleared with streptavidin-agarose beads and then incubated with biotinylated
double-stranded oligonucleotide containing potential IRF binding site within the
ATAC-seq peak at the Cxcl10 Cluster
(5′-CATAGAAAATGTTTTCAAAACCCGCATTCCGCTTATGCTGTCTGGTATCTGAAATAGATCTGTCAGGGGGTCACATTTTATAAGCACCACTTCGTGTTTG-3′)
or Il6 TSS (trimerized 5′-
TGCTGAGTCACTTTTAAAGAAAAAAAGAAGAGT-3′). Proteins bound to the
biotin-labeled DNA were collected by streptavidin-agarose beads, separated by 8%
SDS-PAGE, and analyzed by immunoblotting using anti-mouse IRF5 (Cell signaling),
anti-human IRF5 (Santa Cruz SC-390364) or an anti-T-bet (Santa Cruz; sc-21749)
antibodies.
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2

Western Blot Analysis of Transcription Factors

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The right upper lung tissues were homogenized in the presence of protease inhibitors, and the protein concentrations were determined using NE-PER® nuclear and cytoplasmic extraction reagents (Pierce Biotechnology, USA). The total proteins (50 μg) were loaded onto SDS-PAGE gels. After electrophoresis at 120 V for 90 min, the separated proteins were transferred to polyvinylidene difluoride membranes using a wet transfer method (250 mA for 90 min) [21 (link)]. Nonspecific sites were blocked with 5% nonfat dry milk in Tris-buffered saline containing 0.1% Tween 20 for 1 h, and the membranes were then incubated overnight at 4°C with anti-GATA-3, anti-T-bet (Santa Cruz Biotechnology Inc., USA), or anti-HDAC1–11 (HDAC Family Antibody Set; BioVision, USA) primary antibodies. Horseradish peroxidase-conjugated anti-rabbit IgG was used to detect binding of the primary antibodies. The membranes were stripped and reprobed with an anti-actin primary antibody (Sigma-Aldrich, USA) to verify equal protein loading in each lane. The binding of the specific antibodies was visualized by exposure to photographic film. The densities of the stained bands for T-bet, GATA-3, and HDAC1–11 relative to the staining band for β-actin were quantified with Quantity ONE densitometry software (PDI Imageware Systems, USA).
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3

Immunohistochemical Analysis of Inflammatory Markers

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Slices with 4 µm thickness were arranged on silanized slides (3-aminopropyltriethoxysilane; Sigma-Aldrich Inc., St. Louis, MO, USA), deparaffinized in a 60°C chamber, sequentially hydrated in passages through xylol, absolute alcohol, 70% alcohol, and distilled water. The avidin-biotin peroxidase-anti-peroxidase complex method was used for sample staining. Tissue samples were immersed in 1 mM citrate buffer, PH 6.0, blocked with 3% hydrogen peroxide, and incubated with primary antibodies (polyclonal rabbit anti-iNOS, anti-Nrf2, anti-T-bet, and anti-IL17, diluted 1:100—Santa Cruz, CA) for 1 h. Next, samples were incubated with biotinylated secondary antibodies for 30 min and the avidin-biotin complex for an additional 30 min. Samples were stained by addition of the diaminobenzidine chromogen (DAB) substrate for ∼1 min. The negative control were carried out by omitting incubation with primary antibodies. Tissue sections were examined by light microscopy (400×), and 10 photomicrographs were collected per section (Zeiss Axiostar, Zeiss, Germany).
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4

Western Blot Analysis of Protein Expression

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Whole cell extracts were prepared by lysing cells in Laemmli buffer containing 1% SDS and 2% 2-mercaptoethanol. Lysates from equal numbers of cells were separated by 8 or 10% SDS PAGE, transferred to PVDF membranes (GE Healthcare), incubated with primary antibodies and detected with HRP-conjugated species-specific anti-immunoglobulin light chain antibodies (Jackson ImmunoResearch) and a Luminata HRP substrate (Millipore). Anti-HDAC1 (Abcam, ab7028) and anti-Tubulin beta (Developmental Studies Hybridoma Bank, University of Iowa) were used as loading controls. Anti-AP4 antibody was previously described24 (link). The following antibodies were purchased: anti-c-Myc (Cell Signaling, 9402S), anti-phospho STAT5 (PY694) (BD Biosciences, 611964), anti-Blimp-1 (Genscript, A01647-40), anti-T-bet (Santa Cruz, sc-21003). For translation inhibition and proteasome inhibition, 10 μM of cycloheximide (Sigma) or MG-132 (Sigma) was added to the cell culture. For inhibition of signaling pathways, 20 nM of U0126 (Cayman Chemical), 10 μM of SB203580 (Cayman Chemical), 50 nM of wortmannin (Cayman Chemical), 5 nM of FK506 (Cayman Chemical), or 2.5 nM of rapamycin (Cayman Chemical) was added to the cell culture.
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5

Characterization of Immune Infiltration in OPSCC

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Characterization of lymphocytic infiltration was carried out with triple immunofluorescent staining in 41 OPSCC as described previously [10 (link)] using anti-CD8 (mouse IgG2b, clone 4B11; Novocastra, 1:400), anti-Tbet (rabbit polyclonal, clone H210; Santa Cruz 1:400) and anti-Foxp3 (mouse IgG1, clone 236A/E7; Abcam, 1:200), goat-anti-mouse IgG2b Alexa 647, goat-anti-rabbit Alexa 546 and goat-anti-mouse IgG1 Alexa 488 (all from Molecular probes; 1:200). Based on the morphology of cancer cell nests and autofluorescence of keratinocytes the immune cells per mm2 were manually counted as intraepithelial or stromal using the LSM 5 Image Examiner software (average of five images at a 250× magnification).
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6

Characterization of Copaiba Oil Allergy

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The CO came from Brazil, obtained from the trunk of copaiba trees belonging to Copaifera langsdorffii. It was acquired from Pharmanostra (actual InfinityPharma) (São Paulo, SP, Brazil), lot 16E09-B027-009523. The chemical characterization of this tested CO was performed previously by GC-MS and GC-FID (Caputo et al., 2020 (link)).
OVA was from Sigma Aldrich® (São Paulo, SP, Brazil), Ketamine (10%) from Syntec® (São Paulo, SP, Brazil), and Xylazine (2%) from Ceva® (São Paulo, SP, Brazil). The Star Trek Universal HRP Detection System kit (STUHRP700H, L10) was from Biocare Medical (Pacheco, CA, USA). The primary antibodies anti-GATA3, anti-STAT3, anti-TBET, and anti-FOXP3 were obtained from Santa Cruz Biotechnology (Dallas, Texas, USA), and the anti-IL-33 and the goat IgG hrp-conjugated antibody were from VWR International (Carnaxide, Portugal).
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7

Western Blot Analysis of Protein Expression

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Whole cell extracts were prepared by lysing cells in Laemmli buffer containing 1% SDS and 2% 2-mercaptoethanol. Lysates from equal numbers of cells were separated by 8 or 10% SDS PAGE, transferred to PVDF membranes (GE Healthcare), incubated with primary antibodies and detected with HRP-conjugated species-specific anti-immunoglobulin light chain antibodies (Jackson ImmunoResearch) and a Luminata HRP substrate (Millipore). Anti-HDAC1 (Abcam, ab7028) and anti-Tubulin beta (Developmental Studies Hybridoma Bank, University of Iowa) were used as loading controls. Anti-AP4 antibody was previously described24 (link). The following antibodies were purchased: anti-c-Myc (Cell Signaling, 9402S), anti-phospho STAT5 (PY694) (BD Biosciences, 611964), anti-Blimp-1 (Genscript, A01647-40), anti-T-bet (Santa Cruz, sc-21003). For translation inhibition and proteasome inhibition, 10 μM of cycloheximide (Sigma) or MG-132 (Sigma) was added to the cell culture. For inhibition of signaling pathways, 20 nM of U0126 (Cayman Chemical), 10 μM of SB203580 (Cayman Chemical), 50 nM of wortmannin (Cayman Chemical), 5 nM of FK506 (Cayman Chemical), or 2.5 nM of rapamycin (Cayman Chemical) was added to the cell culture.
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8

IRF5 and T-bet Binding Assay

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ONP assays were conducted as previously described 51 (link). Briefly, nuclear extracts were
precleared with streptavidin-agarose beads and then incubated with biotinylated
double-stranded oligonucleotide containing potential IRF binding site within the
ATAC-seq peak at the Cxcl10 Cluster
(5′-CATAGAAAATGTTTTCAAAACCCGCATTCCGCTTATGCTGTCTGGTATCTGAAATAGATCTGTCAGGGGGTCACATTTTATAAGCACCACTTCGTGTTTG-3′)
or Il6 TSS (trimerized 5′-
TGCTGAGTCACTTTTAAAGAAAAAAAGAAGAGT-3′). Proteins bound to the
biotin-labeled DNA were collected by streptavidin-agarose beads, separated by 8%
SDS-PAGE, and analyzed by immunoblotting using anti-mouse IRF5 (Cell signaling),
anti-human IRF5 (Santa Cruz SC-390364) or an anti-T-bet (Santa Cruz; sc-21749)
antibodies.
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