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6 protocols using anti cx3cr1

1

Cytokine Profiling in Mouse Brain

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400 μg of protein from the cytosolic fraction of brain tissue homogenates (n=4 per condition) were used for analyzing relative levels of 40 different mouse cytokines using a Mouse cytokine panel array (R&D systems, Minneapolis, USA) following the instructions of the supplier. The binding of the detection antibody was detected in a VersaDoc gel-imaging machine (BioRad) and quantified using Quantity One software (BioRad). Fractalkine (CX3CL1) and fractalkine receptor (CX3CR1) protein levels were measured by immunoblot and immunocytochemical analysis in the cytosolic and particulate fractions of mouse brain homogenates. The antibodies used for both analyses were anti-CX3CL1 (M-18, Santa Cruz) and anti-CX3CR1 (Abcam). Analysis of β-actin (Sigma) levels was used as a loading control.
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2

Characterization of Cell Spreading Assay

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Spleen mononuclear cells MNCs isolated from all the experimental groups were resuspended in RPMI 1640 medium containing 10% FBS and 1% penicillin/streptomycin and seeded on round 12-mm diameter coverslips in a 24-well plate coated with 5μg/ml recombinant mouse VCAM-1 (R&D Systems) for 2 h at 37°C. After two washes with PBS, the cells were fixed with 4% paraformaldehyde for 10 min at +4°C. The cells were rinsed three times with PBS and then incubated in PBS/0.1% Triton X-100 (Sigma-Aldrich) for 10 min. After three rinses with PBS and incubation with 2% BSA to block nonspecific staining, the cells were stained with 0.165 μM Alexa Fluor 546 Phalloidin (Thermo Fisher Scientific, France) for 60 min at 37°C. The primary antibody anti-CX3CR1 (Abcam) was used for immunostaining. After the incubation, slides were washed with PBS-T and probed with fluorescence-conjugated secondary antibodies for 1 h at RT. The cell nuclei were counterstained by Vectashield mounting medium with DAPI (Vector). Cells with flat morphology or lamellipodia were positively scored for spreading.
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3

Immunofluorescence Analysis of CX3CL1 and CX3CR1 in IPF

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We evaluated 4 IPF cases and 5 controls using 3 µm thick FFPE lung sections. We used rabbit anti-CX3CL1 and anti-CX3CR1, and goat anti-CX3CL1 (Abcam, Cambridge, United Kingdom) primary antibodies, detected with anti-rabbit IgG Alexa fluor (AF) 647 and anti-goat IgG AF 546 (Jackson Immunoresearch, Baltimore, USA). We analyzed 5 lung fibroblast lines derived from IPF lungs, (obtained as described in Becerril et al. 1999 24 (link)); healthy lung fibroblasts (HPF and NHLF) were obtained from Promocell (Heidelberg, Germany), Lonza (Basel, Switzerland) and primary cultures from cadaveric donation (FN-2-13). 20,000 fibroblasts were seeded in coverslips. The next day, cells were fixed with cold methanol/acetone. After blocking (1X Powerblock™ (Biogenex, Cal. USA) + 0.5% Triton X-100), samples were incubated ON with primary antibodies, then for 1 hour with fluorescent secondary antibodies, and counterstained with DAPI. Fluorescence was evaluated with an FV-1000 laser scanning confocal microscope (Olympus, Tokyo, Japan).
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4

Investigating Signaling Pathway Activation

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Western blotting was performed on cytosolic cellular extracts. Cells were washed with cold phosphate-buffered saline and lysed for 15 min on ice in 0.5 ml of lysis buffer containing protease and phosphatase inhibitors. Cell lysates were clarified by centrifugation (4 °C, 15 min, 12,000 rpm), and protein was subjected to 10% sodium dodecyl sulfate-PAGE (SDS-PAGE) and transferred to a nitrocellulose membrane using a wet transfer system. Membranes were incubated with 5% skim milk dissolved in TBS plus 0.05% Tween 20 (TBST) for 1 h to block nonspecific protein-binding sites. Then, the membranes were incubated with anti-CCRL2 (Abcam, no. ab88632), anti-CX3CR1 (Abcam, no. ab8021), anti-p38 MAPK (Abcam, no. ab197348), anti-ERK (Abcam, no. 196883), anti-AKT (Abcam, no. ab8805), anti-phospho-ERK (Abcam, no. ab50011), anti-phospho-AKT (Abcam, no. ab81283), anti-phospho-p38-MAPK (Abcam, no. ab47363), and anti-GAPDH (Abcam, no. ab181602) antibodies at 4 °C overnight according to the manufacturer’s instructions. The membranes were then washed with TBST and incubated with a secondary anti-rabbit Ab conjugated to HRP (Cell Signaling Technology, no. 7074s) at room temperature. The signals were detected and analyzed by a chemiluminescence imaging system (ChemiScope5600, CLINX, Shanghai, China), and each experiment was performed in triplicate.
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5

Antibody Sourcing for Protein Analysis

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Anti-TUBB and anti-ACTB were purchased from Developmental Studies Hybridoma Bank (Iowa City, IA). Anti-rabbit IgG HRP-linked antibody, anti-phospho-CHEK2, anti-phospho-CHEK1, and anti-CHEK1, antibodies were obtained from Cell Signaling Technology (Danvers, MA). Anti- CX3CR1, anti-phospho-ATM, anti-phospho-PRKDC, anti-PRKDC, anti-ATM, and anti-phospho-H2AX antibodies were obtained from Abcam (Cambridge, MA). Anti-mouse IgG HRP-linked antibody, anti-phospho-ATM, anti-CHEK2, anti-MYC, and anti-phospho-H2AX were obtained from Santa Cruz Biotechnology (Santa Cruz, CA). Alexa Fluor 488 goat anti-mouse IgG and Alexa Fluor 546 goat anti-rabbit IgG were from ThermoFisher Scientific (Waltham, MA). Anti-GPR65 and anti-FFAR4 antibodies were obtained from One World Lab (San Diego, CA). Anti-RAD50 antibodies were purchased from NeoBiolab (Cambridge, MA).
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6

Multicolor Immunofluorescence Imaging

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Selected antigens were labeled with the use of antibodies: anti-CD34 (unconjugated, Dako, Glostrup, Denmark), anti-CX3CR1 (unconjugated, Abcam Inc., Cambridge, MA, USA), anti-cytokeratin 7 (unconjugated, Dako). To visualize presence of unconjugated antibodies Alexa 488 and Alexa 647 were used. DAPI has been used to counterstain nuclei. The staining protocols were based on producer's manuals. We have selected pairs of antigens to be visualized on a single section: CD34 and CX3CR1, and cytokeratin 7 (CK7) and CX3CR1. The slides were investigated and microphotographed on a confocal microscope (FV1000 Olympus).
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